Tuesday, November 29, 2011

Ayn Rand: Straw Vulcan

Been skimming skepticon videos on youtube, and I came across this little gem. It's long, but you may want to give it a watch in your spare time one day. It's quite informative:

Contrarily, if that's too long for you, you can just read this page instead. It's the gist of it (and it's also the source of the term used in the video).

But anyways, I've been researching Ayn Rand these last few days, out of bile fascination, and as I was watching interview clips with her (also on youtube), I realized something: Ayn Rand is a straw vulcan.

First thing's first: what *is* a "straw vulcan?" If you watch the video (or read the TVtropes entry), you'll see. But in case you're just that short on time, here's the rough explanation (from the link):

A straw man used to show that emotion is better than logic. It starts by having characters who think "logically" try to solve a problem. And they can't. Either they can't find any answer, or they're caught in some kind of standoff, or they're even stuck in a Logic Bomb-type loop. Once this is established, someone who uses good old human emotion comes up with a solution that the logical thinker can't. This provides An Aesop that emotion is superior and that the logical thinker shouldn't trust logic so much. This is, of course, a broken Aesop. Fiction often gets the concept of logic wrong in a number of ways.

Anyways, I was watching this smack piece against Ayn Rand, and one of the interviews featured therein stuck with me a little:

At approximately 2:48, the following exchange occurs:

Interviewer: "Christ -- every important moral leader in man's history --- has taught us that we should love one another. Why, then, is this kind of love, in your mind, immoral?"

Rand: "It is immoral if it is...placed above oneself."

It's not exactly the same thing as a straw vulcan....but it's very close. "Love" is a weakness; reason is being misapplied in order to arbitrarily "rule out" things like human emotion and love as "weakness." The only difference is, in the case of the straw vulcan, it's a poor literary technique used to set up the character for a fall, to demonstrate that pure reason supposedly doesn't work. In this case, Rand seems almost completely unaware of the irony of her position....Ayn Rand's philosophy of "objectivism" assumes that there are humans who are "self-sufficient" in the sense of being completely, universally independent of other humans to provide for their own basic needs.

The problem is, the capitalist system (around which her philosophy is necessarily centered, in defense --- or rather, worship --- of property rights, even to the exclusion of the value of human life*) is based on the idea that humans will require services of one another. You can't get rich without the cops protecting your property and other people's taxes paying those cops' salaries. You can't run a business without other people who are poor enough to want to work under you. You can't even go out to eat, or work on your car, unless you either (A) have a skill set pertaining to whatever activity you're carrying out (nobody has professional experience in all possible fields, so reductio ad absurdum here is an inevitability), or (B) know someone who has that knowledge and is willing to share it with you or use it on your behalf.
The capitalist system is based on this interaction and is designed to facilitate it. Hence, capitalism = human interdependence, not independence. We depend upon each other. That's not weakness, it's human nature.

All of which is to say....Rand is a straw vulcan because she portrays herself as "reasonable" and "logical" to the exclusion of the "weakness" of human emotions such as love and compassion, without realizing that a truly reasonable person would acknowledge that human emotion is a necessary component of human functionality, and that individual prosperity is inherently linked to social prosperity because of our need for each other's skills and company.

Now....before you Ayn Rand fans go bashing me for "not understanding" her philosophy, or for rejecting her out of hand....that's not to say that I am completely trashing her. This is not meant as a political statement. Another video that caught my eye was this one:

Now I'm no Ralph Nader fan by any stretch, but I did find myself swayed ever-so-slightly by his argument here. He, too, finds her philosophy "abhorrent," but he also provides an interesting justification for why she may have come about with such a philosophy: having lived with a communist background, she has seen the extreme end of what complete and utter forced selflessness can produce, and so has "lived the extreme." Nader's theory (which I find, in its simplicity, surprisingly satisfactory) is that her overly-selfish philosophy is a sort of over-reaction against her experience with communism and socialism. I can understand that to a degree, and so with that in mind I can say I respect Ayn Rand a little more than I did before --- even though I still disagree with pretty much all of her philosophy.

--Tim D.

*=in truth, this is a criticism that is more aptly leveled at her present-day followers and worshippers, not as much to the woman herself (although a case can be made thusly). In any case, I'm using it here more as a smack against her followers than against her personally.

Sunday, November 27, 2011

Evangelical Christians, Please Watch This

Not because I think it's likely to change your mind about anything, but because it will help you understand us a little better.

Tuesday, November 22, 2011

The Beginning of Life and The "Potential Argument"

We're gonna talk about abortion for a minute. Yep. But not in the usual way; I'm not going to debate the pros and cons thereof, or make my case for or against it. Rather, I just want to address one small facet of a particular argument --- actually, two small facets of two different arguments that are basically two sides of the same coin.

Confused yet? Well, I'm referring to the "Potential Argument." It goes something like this:

"Life begins at conception. Once an egg is fertilized by a sperm and becomes a zygote, if it's left alone, it will eventually become a person with thoughts and feelings. Therefore, a zygote is equivalent to a person."

This argument seems to have a logical ring to it on the surface, but for some reason I've always been reluctant to accept it --- it's as if my brain senses some illogical, irrational quality beneath the surface of that soundbyte exterior. I could never really put my finger on why, until my girlfriend and I were talking the other day (about what, I don't recall) and, in the process of trying to make some point to her, I stumbled upon an unfamiliar analogy (note, I don't speak quite this formally in person, this is sort of a reconstruction for clarity):

"I think people who use the potential argument are committing a basic logical fallacy in equating the zygote with the human. For example, when they portray parents as irresponsible for wanting to have an early-term abortion, they often use examples that apply specifically to actual, "born" children --- they might say, for instance, that it's tantamount to emotional child abuse to tell, say, a five-year-old, "I shouldn't have had you." And they'd be correct on this count. That's a cruel thing to say to a child, that you don't want them, or that they were a mistake. But then, let's put the shoe on the other foot: let's re-wind to the night the child is conceived. The parents are about to have sex and one says to the other, "you know what? Let's wait, I'm not ready to have kids yet," or perhaps, "I don't want a kid right now."

Is that the same thing as telling a child you've already had that you "don't want" them?

If you answered yes, then I disagree. I think it's rather different because, in the former case, we're speaking of a person who exists now and thus has consciousness and feelings and such. In the case of the latter, we're speaking of an event which has yet to take place. That may seem like a semantic distinction, but I do not think I'm being wildly impractical when I say that we should wait until a given person exists in order to bestow him or her with, say, legal rights. Otherwise we are faced with the criteria of how to determine when and where a person will guaranteed to come into existence in the future (which is itself impossible, as it requires us to foresee the future with certainty). This opens up an entirely new debate in and of itself, which I won't go into here for reasons of brevity. But suffice it to say that, whichever side of this argument you find yourself on, it should be agreed that waiting until a person actually exists is the best, most guaranteed way to know that they are alive. Otherwise we must afford an infinite number of "potential citizenships" to an infinite number of people who may or may not one day be born and given names and such. This line of reasoning goes on and on...but it's beside the point.

If your answer to the original question is "no," then why? Is there some fundamental difference between a child and a zygote, such that telling a zygote you "don't want" it before it exists is different from telling a child you "don't want" it before it exists?

We can say that a human child is just a different stage of a zygote....but then, why this distinction? What does it matter whether I'm talking to a zygote or a child, if they're the same thing? Furthermore, if a zygote is a child because of the potential argument --- if we determine that a zygote is now a human child based on the argument that, if left alone, it will eventually become a human child --- then how is it that it is not, for example, just as much of a crime to not conceive a child as it is to terminate a pregnancy that has already been conceived? If two people, who are attracted to each other, are left alone in a room and left to their own biological designs, they will procreate and conceive offspring. So using this same reasoning, can we also not confirm that this "child" exists in some abstract, metaphysical sense before the pregnancy even begins? Is it then a "crime" to interrupt the two as they attempt to reproduce? Does that constitute "playing god" with nature?

I guess a simpler way of putting it would be....it seems to me that this argument, the "potential argument," relies on the establishment of the "child" not just as a physical thing that exists, but also as a conceptual entity. Some of the claims take into account the beginning of the physical entity ("life begins at conception"), while others refer to the "person" in the abstract (for in what other sense than the abstract is a feelingless, psycheless, consciousness-less mass of cells equivalent to a human being with feelings, a psyche and a consciousness?). The problem is then exacerbated when people equivocate between these two concepts --- the physical "child" and the conceptual "person" --- and argue from either point as though they are one and the same. I think that's the reason this argument doesn't float in pro-choice circles; because, on some level, people are aware of this equivocation, they sense it, and they innately understand that it is wrong, even if they don't understand why. And they, like myself, may become temporarily misguided and fall for other arguments as they try to understand why they feel that nagging sense of "wrongness." There may be some crude "life" which begins at conception, but the conceptual "person" that we "know" begins once the fetus has achieved maturity and is capable of interacting with us socially.

So in closing, you might say that my conclusion is thus: Life, in some sense, does begin at conception. But a person does not begin until the conceived organism has developed the capacity to maintain an ego. The zygote, then, could be described as the "shell" that the person itself will someday inhabit, but not the person him- or herself. For if we ignore the significance of the ego in determining what is a "person" and what is not, then we could simply say that bacteria (or any other non-human organisms) are "people" too, because they are alive, even if only in a most primitive sense.

"Life" is, quite simply, not the only issue here. And a failure to recognize this is almost a sure-fire guarantee that any given argument --- for or against abortion --- will also be a failure.

--Tim D.

Monday, November 21, 2011

I Missed AlabamAtheist's Birthday....

10/07/11 was the official 1-year anniversary of this blog! W00t!

...I just realized this, so I didn't have time to really think of anything to do to celebrate. Oh, well. Maybe by this time next year I'll have a higher posting average than once a month? Derp. Thanks for reading, all 2 or 3 of you out there (myself included)! It's been a....decidedly unproductive year. Let's hope I can change that this year~

--Tim D.

In Case You Missed It This August....

Remember, "Black Box Dilemma" dropped in August and is still available (free) by request! Here's another sample, the apparent favorite track off of this album:

Thursday, November 17, 2011

(Yet) A(nother) Defense of Darwinian Evolution

Leave it to Mr. McLatchie of Crossexamined.org to fly right under just about every point on that list I just made....yeesh. Alright, where do I begin? First:

Since the body plan of organisms is established right at the beginning of development, the types of changes which are required to evolve a novel body plan are the very kind which are least likely to be tolerated by organisms.

I don't know why he's saying this again. He actually said this in the first article, which I took pains to re-acknowledge in my latest response. Here is what I said (or, if you don't believe me, you can go read it yourself again, here):

...with regard to the change in "body types" being unlikely: yes, in a single generation, or in even several successive generations, a population is very, very, very unlikely to exhibit any major changes to its morphological arrangement --- limb placement, the addition or subtraction of major features (such as a tail, limb, eye, or fin), and so on --- but that is not what happens. The "mutations" which Mr. McLatchie refers to as "unlikely to be beneficial" during embryonic development are, of course, generally not responsible for the major morphological changes observed in evolution! There is very little, if any, real "body plan mutation" -- in fact, there is much debate over whether such a scaled mutation is even possible.

So now that we've cleared that up (again, and hopefully for the last time), let me say it loudly and clearly once more: embryonic mutation is *not* considered a primary vehicle for natural selection under Darwinian evolutionary theory. Anyone who tells you it is, is talking about a different school of thought within the evolution debate than the one I am defending here. Within the school of which I consider myself a part (the "Darwinist" school), there is debate over whether this is even possible to the extent that a beneficial mutation(s) is even likely to occur with enough frequency to account for any degree of major --- or minor --- evolutionary change.

If Mr. McLatchie raises this point against me again, as if I had not just made it myself for a third time, I will simply point to this quotation here and not explain it any further. I hate wasting my energy more than anything.

Second, Mr. McLatchie scolds me for not having read his back-catalogue of arguments from his other blog:

Tim gives us three pieces of evidence for neo-Darwinian evolution that I am allegedly “wholly unaware of”. This is a curious claim, since his third example I have already explicitly discussed in my writings (towards the end of this post).

 I would like to extend a hearty public (albeit somewhat snide) apology to Mr. McLatchie for not having read his blog. I don't follow it (in fact, I didn't even know it existed until a few months ago), and I certainly haven't had all the time I'd like to have properly browsed it. But for the sake of this particular discussion, it's safe to assume here on out that, if you haven't written it up in one of these articles, I probably haven't read it. So if you refrain from assuming my familiarity with all of your previous writings, and take pains to make your individual points as they apply, then this will go a lot more smoothly in the future.

Third: Mr. McLatchie criticizes the Nguyen et al paper (or rather, my interpretation --- or better, his misrepresentation of my interpretation --- of it), saying that:

On the bacterial flagellum, amazingly, Tim cites a paper (Nguyen et al., 2000) which demonstrates the very opposite from the line of argument he wishes to take! The paper suggests “that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems.” So that research is not much use to Tim’s case (which requires that the flagellum evolved from the Type-III secretion system).
 ....with regard to the bold-faced segment, well, I don't know any nicer way to phrase it than to say that Mr. McLatchie is just plain flat-out wrong here. And I'm not sure why or how he became so wrong. Because I took great pains to state my *actual* case clearly in my last response. Here is what I said (again, click my earlier link to go read it for yourself in context):

What the consensus tells us is that the flagellum and the T3SS probably each had an early precursor from which they diverged, which shared many (but not all) of the necessary genes to express the complete flagellum.
 That is actually quite different from Mr. McLatchie's presentation of what I said. According to him, I'm claiming that the T3SS came first and later evolved into the flagellum. What I actually said was that, regardless of the order in which the two specifically evolved, and based solely on the written conclusion of the study I quoted (i.e. their words, not mine), the T3SS and flagellum evolved not from one another but from a similar construct with many (but not all) genes homologous to parts of both the T3SS and flagellum. In this particular case, there would actually be less evolutionary change necessary to go from the simple homologous ancestor construct to the T3SS and/or flagellum, because a percentage of the necessary genes were already in place in either case. The Matzke model, whether or not it describes an actual account of the history of the T3SS/flagellum relationship, shows that it is at the very least possible, in principle, for such change to occur. Therefore, a smaller degree of change would be mathematically more probable anyway. That was my point.

If Mr. McLatchie would prefer to respond to what I actually said, instead, then that would be fine of course. I don't have much time to waste on straw men, however.

Next point; I won't go into the much larger debate of Lamarckism vs. Mutationism vs. Darwinism vs. etc. so on and so forth; in this paragraph, Mr. McLatchie sums up the current scene of this debate pretty well:

What Tim is describing as “mutationism” here is probably closer to some forms of neo-Lamarckism which maintain that mutations arise not randomly, but in response to environmental pressures. One classic study (Luria and Delbruck 1943) is traditionally cited in these discussions in support of the traditional view that mutations occur irrespective of environmental concerns. This study involved the exposure of a strain of E. coli to bacteriophages and demonstrated that the probability distribution for the number of mutants exhibited the characteristics expected only if random mutations had been present prior to exposure to the phage, apparently ruling out the proposition that the mutations occurred as a result of the phage. That being said, there have been a number of interesting papers that have been published in recent years which report regulation of mutation rates and localised variation in response to stress (see, for instance, Galhardo et al., 2007 and Rando and Verstrepen, 2007).

I of course take no issue with that paragraph. However, as a commenter helpfully pointed out to me in another posting, Mr. McLatchie seems to have (once again) completely missed my point with this criticism:

A further confusion on Tim’s part pertains to his assertion that “An example of [speciation] would be if a particular population of a certain species had mutated sex cells that prevented them from forming offspring with members of other populations of that species; we would then say that this population was ’speciated’ from all other populations.” Mutations in the germ cells which negatively affect an organism’s capacity to reproduce are not going to become fixed in any population because a key part of this process is the ability to reproduce. Does Tim really think this is a serious argument? In any case, Tim seems to think that I somehow have doubts about the occurrence of speciation; but such skepticism is harboured nowhere in my writings.

I was referring to the speciation of populations, not of individual organisms. My argument here pertains to the speciation of entire groups (i.e. populations) of organisms which, while able to reproduce amongst themselves, cannot reproduce with other populations of the same "species." Hence, the differentiation --- or "speciation." Mr. McLatchie's argument that "mutations...which negatively affect an organism's capacity to reproduce are not going to become fixed in any population" only applies here if we're talking about individual organisms. As long as each organism is capable of reproducing within a select population, it doesn't matter what its reproductive compatability is with regard to other populations from which it is genetically isolated (as it has no means of contacting them in the first place, much less breeding with them). So this point is lost on Mr. McLatchie as well.

Skipping ahead a little, to the manatees. I had pointed out the various land-mammalian features of these sea-dwelling features, paired with their apparent lack of need for said features as a mild form of suggestive evidence for the idea that they may be related to land mammals (as, if they are not, then it becomes even more important to explain why they have these features; if they used to be land mammals, and are not anymore, as Mr. McLatchie suggests below, then that would make for a prime example of large-scale evolution, would it not? A land mammal evolving into a completely sea-dwelling mammal with vestigial limbs and parts as evidence of its alteration). Mr. McLatchie writes:

Indeed, it is true that these sea cows possess elephant toenails on their flippers. But this only succeeds in bringing us back to the old “common features = common ancestry” argument. It is also by no means implausible that these organisms were once able to walk on land.
 Again, as mentioned above, this is indeed part of my original argument --- that manatees are in some way related to land mammals! If a manatee used to be a land mammal, then that would make it the evolutionary successor of a land mammal, would it not? Hence, Mr. McLatchie makes my point for me.

With regard to ape chromosome fusion, Mr. McLatchie writes:

To make much of the 2q13 interstitial telomeric sequence and portray it as typical of what is observed in chimp and human genomes may be considered careful cherry-picking of data.

To "make much" of it...."may" be "considered" careful cherry-picking of data. Notice the careful use of these terms so as not to imply a definite conclusion? Mr. McLatchie commits the fallacy of assuming that I offered this evidence as, in itself, conclusive. It is simply suggestive. He doesn't do much to negate my point here other than to point out that, in itself, it is not 100% conclusive. Well, I could have told you that! The closest thing to any single fact about evolution that can be construed as anything close to "100% conclusive" is the classically-cited lack of, say, rabbits in the Cambrian layer. Find one rabbit in the Cambrian and you ruin the entire theory of evolution. And yet to this day, no rabbits in the Cambrian. That in itself is rather convicting evidence....but again, only in context with the rest of the theory! For without the rest of the theory, we wouldn't know *why* the lack of rabbits in the Cambrian is proof.

No, Tim, this is a retrospective analysis based on sequence homologies. At the very best, it would demonstrate common ancestry of the globin protein family (but even that conclusion is suspect).

...I would ask Mr. McLatchie if he even read what I said in any detail. "At the very best, it would demonstrate common ancestry of the globin protein family." That is exactly what I said! My original quote, which (oddly) Mr. McLatchie cites in his response:

there is evidence that the four protein chains in current human adult globins actually originated from an ancestor genome which “split” around 500,000,000 years ago into two parts; each part then later mutated separately and became a different cluster. This happened again around 400,000,000 years ago, and the alpha gene mutated again, following a similar path and giving us the zeta chain. This much is actually supported by contemporary phylogenetic analysis, as well — other animals descended from those who existed around the time of the genome split (and which were associated with our ancestral line) also demonstrate this same split, and the same chromosomal arrangement of these genomes.

The fact that this same sequence split is manifest across species lines (and in species which other evidence suggests to be distantly related) is evidence of evolutionary speciation on a large scale. And the further fact that these analyses match up with our other evidence indicating the approximate time of speciation between those species is yet another point of interest. If Mr. McLatchie had read the Dawkins article I linked to, he would've read this passage:

Here’s the fascinating point. Careful letter-by-letter analysis shows that these different kinds of globin genes are literally cousins of each other, literally members of a family. But these distant cousins still coexist inside our own genome, and that of all vertebrates. On the scale of a whole organism, the vertebrates are our cousins too. The tree of vertebrate evolution is the family tree we are all familiar with, its branch-points representing speciation events — the splitting of species into pairs of daughter species. But there is another family tree occupying the same timescale, whose branches represent not speciation events but gene duplication events within genomes.
The dozen or so different globins inside you are descended from an ancient globin gene which, in a remote ancestor who lived about half a billion years ago, duplicated, after which both copies stayed in the genome. There were then two copies of it, in different parts of the genome of all descendant animals. One copy was destined to give rise to the alpha cluster (on what would eventually become Chromosome 11 in our genome), the other to the beta cluster (on Chromosome 16). As the aeons passed, there were further duplications (and doubtless some deletions as well). Around 400 million years ago the ancestral alpha gene duplicated again, but this time the two copies remained near neighbours of each other, in a cluster on the same chromosome. One of them was destined to become the zeta of our embryos, the other became the alpha globin genes of adult humans (other branches gave rise to the nonfunctional pseudogenes I mentioned). It was a similar story along the beta branch of the family, but with duplications at other moments in geological history.
Now here’s an equally fascinating point. Given that the split between the alpha cluster and the beta cluster took place 500 million years ago, it will of course not be just our human genomes that show the split — possess alpha genes in a different part of the genome from beta genes. We should see the same within-genome split if we look at any other mammals, at birds, reptiles, amphibians and bony fish, for our common ancestor with all of them lived less than 500 million years ago. Wherever it has been investigated, this expectation has proved correct. Our greatest hope of finding a vertebrate that does not share with us the ancient alpha/beta split would be a jawless fish like a lamprey, for they are our most remote cousins among surviving vertebrates; they are the only surviving vertebrates whose common ancestor with the rest of the vertebrates is sufficiently ancient that it could have predated the alpha/beta split. Sure enough, these jawless fishes are the only known vertebrates that lack the alpha/beta divide.

That is a very, very interesting coincidence, given Mr. McLatchie's assertion that these speciation events never took place! I hold here that divergent evolutionary speciation is a much better, much more concise, and much more roundly-supported explanation for this convergence of otherwise very mysterious "coincidences." So how does Mr. McLatchie account for this interesting coincidence, given a complete lack of mass-scale speciation as he has hypothesized? Or can he, even? I wonder. He seems to be a proponent of Intelligent Design Creationism; do they hold this as a great mystery of life? Or do they have some explanation for it? You may not be able to tell through my somewhat snarky tone at the moment, but I'm genuinely interested to hear of it if they do.

I mean, he talks of globins as if I'm saying they just evolved willy-nilly overnight. Each of these events is believed to have happened over 100 million years apart! And the degree to which he attributes them to a single chance mutation is reminiscent of the "what use is half an eye?" argument that creationists used to use before common sense gave us the answer: "crude function out-competes no function at all," i.e., it's better to see badly than not see anything. But that's another debate altogether, and I don't want to get TOO much farther off topic in this posting.

Speaking of Intelligent Design Creationism....McLatchie writes:

[C]ommon ancestry is not, in and of itself, a causal process. Common descent could be correct but the neo-Darwinian mutation/selection mechanism totally wrong. Since ID — in its purest sense — only claims to be able to detect patterns in nature which are best explained as the product of an intelligent cause, the theory is silent on the issue of common ancestry.What ID does challenge is the materialistic view of evolution which envisions the origins and development of life on earth as being the product of the mindless and impersonal forces of nature.
For my closing, I would like to ask two questions....

(1) So you admit, then, that IDC cannot explain why we see common descent?
(2) If evolution happened, it happened; it doesn't matter whether god did it or whether it happened because of some hidden inevitability given the laws of physics, enough time, and enough opportunity. Even if we say "someone" (i.e. god) created life, or that this "someone" somehow engineered the process of evolution, that's completely irrelevant information unless we can say HOW they did it. Science is not a question of, "who did it? Nature or god?" That's a false dichotomy painted by IDC proponents and perhaps some overly fierce atheists. No, the central question of any explanatory theory is, "how?"

That is my biggest problem with IDC, is that its proponents find themselves almost completely unconcerned with the methodology of "how," only with the ideological ramifications of accepting the existing theory of evolution. In fact, it's as if the entire IDC movement exists solely as a counterpoint to the perceived moral and ideological ramifications of the existing evolutionary theory. Look, I really really hope the Christian god isn't real, but if he was, I would have to accept that, regardless of the ideological ramifications it would bring to my current worldview. To oppose the materialistic theory of evolution because of some ideological ramification is just, well, dishonest. Dishonest, and stupid. It's like saying, "guns don't work because if you shoot someone in the face, that's wrong."

Ideology has nothing to do with it, at least for me.

--Tim D.

Tuesday, November 15, 2011

A(nother) Defense of Darwinian Evolution

(this is a rather late response to a piece by Johnathan McLatchie at Crossexamined.org)

First things first....for all his criticisms, Mr. McLatchie did concede one point in favor of my earlier essay, which was that I had demonstrated small changes over time in a satisfactory manner:

Tim gives us one or two other uncontested examples of the occurrence of natural  selection in the wild, reminding us that “[Evolution] is about divergence, not  progression. To ‘evolve’ does not mean ‘to get stronger’ or ‘to get better,’ or to ‘improve’. It simply means to ‘change.’” Well, no one is going to dispute that living species change over time, or even that this change is, in part, facilitated by natural selection.

So I will consider my introductory point "made" and will not waste any more time on it. Alright! Moving on...


...with regard to the change in "body types" being unlikely: yes, in a single generation, or in even several successive generations, a population is very, very, very unlikely to exhibit any major changes to its morphological arrangement --- limb placement, the addition or subtraction of major features (such as a tail, limb, eye, or fin), and so on --- but that is not what happens. The "mutations" which Mr. McLatchie refers to as "unlikely to be beneficial" during embryonic development are, of course, generally not responsible for the major morphological changes observed in evolution! There is very little, if any, real "body plan mutation" -- in fact, there is much debate over whether such a scaled mutation is even possible. Dr. Richard Dawkins goes into the various sides of this debate in his book, The Blind Watchmaker, detailing the "mutationists" (who believe that mutations are somehow naturally inclined toward "beneficiality" or "directional evolution") and the "Darwinian evolutionists" (his own school, which holds that (A) mutations are introduced basically at random, not in any sense "directional" or otherwise biased towards improvement, and (B) the process of embryonic development may "restrict" certain kinds of change such that they are basically impossible --- such as wings growing on the backs of organisms in the human lineage, something which has never been observed in the fossil record). Any such sudden, large-scale mutation --- even assuming it were possible --- occurring in a single generation would be so large that it would be, as Mr. McLatchie indicates, very, very unlikely to be beneficial, and would be significantly more likely to inhibit or outright kill the fledgeling organism. But of course, that is not the type of mutation we are addressing when we refer to "macroevolution."

No....as I said before, "macroevolution" (as creationists describe it) is literally just "microevolution," "stacked" upon itself and extended over a long period of time; but more importantly, when macroevolutionary changes (as scientists describe them) occur, they occur on the same level as microevolutionary changes --- they do not suddenly appear as massive mutations, they represent a "milestone point" of sorts wherein the "new" species is "officially" no longer able to interbreed with the "parent" or "ancestor" species, due often to a simple, small mutation that was preceded by many other small mutations. An example of this would be if a particular population of a certain species had mutated sex cells that prevented them from forming offspring with members of other populations of that species; we would then say that this population was "speciated" from all other populations.

Argue that "macroevolution" doesn't occur, fine; but to deny that they are the same process, differing only on a scale of time and succession, renders this discussion impossible, because that's what scientists are talking about when they say "macroevolution." That's the only way macroevolution can happen, is through the lens of microevolution. If you deny this simple fact, then at the risk of being forward I must say that we are no longer talking about the same concept. And so it is this conjoined concept that I will be addressing henceforth.


With that considered....almost any "microevolutionary" mutation is, in theory, possible --- which is to say, a reptile's claws may change in size from generation to generation, and if the change proves beneficial, this mutation may be preserved. Or, a bird's feathers may change ever-so-slightly in size or color or length. This change is "microevolutionary," indeed --- too small to justify claims of speciation in any short number of generations. However, this change is also cumulative, and this much can (and has) been demonstrated before, in cases such as Darwin's finches, the Endler guppy experiments, and the aforementioned Pod Mrcaru lizards, all of which are denied by evolution-deniers (and yet for reasons that are inconsistent with the Darwinian understanding of evolution). Each of those examples demonstrated cumulative evolutionary changes --- small increases, "stacked" upon one another to create greater changes to specific features. If bigger heads improve surivival in a population, than any increase in head size will likely be preserved (because the conditions necessary for survival will lead to nature unconsciously "embracing" traits which, to whatever degree, cause an organism to become more suited to those conditions), thus these adaptations will "stack" to result in a much larger net increase in head size across many generations, leaving the descendants with noticeably larger heads than the ancestors. And at no point does this change suddenly cease to be possible; it's a matter of the degree of change, not the type of change.

But again, all those are small, "microevolutionary" changes. Think of this, however: we can prove, easily, that small change is possible. And small changes are cumulative. Therefore, if they accumulate, we will see a much greater change overall than that exhibited by single mutations in short generational distances. It is by this method --- slow, gradual change, not sudden, rapid, powerful mutation --- that we see major changes in an organism's morphology. So the "dilemma," as Mr. McLatchie has painted it, is not in fact a dilemma at all; he seems to be mistaken about the very method by which gradual change accumulates. In fact, he seems to imply that there is a point at which this change ceases to be cumulative --- that a beak can change in size, or a foot can change in size, but not both; that an eye can become more or less potent, or legs can become shorter and more powerful or longer and more limber, but not both. This is false. Small changes --- wherever they occur on the body --- are cumulative, because genetics are cumulative. They start with the same embryonic blueprint, and genes add and alter additional features --- this is one way that we can detect the "trail" of evolution through the study of DNA relations between species. Thus, if small changes to individual regions of the body are possible, it logically and demonstrably follows that large chains of change can gradually accumulate which appear to affect entire regions of the body, or even the entire body itself. This is yet without even considering literal examples in which this happens --- we can arrive at this conclusion based on reasoning (and the fact of microevolution) alone.


Speaking of literal examples....there are three somewhat famous examples which Mr. McLatchie seems wholly unaware of. At the very least I find it odd that he did not address them, even if only to try and discount them:

-) The Oenothero gigas (follow the link, then C+F "O. gigas"), a form of evening primrose, was successfully artificially speciated from the evening primrose, such that it can successfully breed with others of its kind but it cannot breed with the original species from which it was speciated.

-) Manatees (follow the link, then C+F "manatee"), in a display of common kinship with land mammals, have elephant toenails on their flippers, as well as an internal skeleton that is completely homologous to humans and other terrestrial tetrapods; it contains rudimentary pelvic bones (especially odd for a creature that supposedly has, neither currently or historically, the need of a pelvic region nor a relation to any organism that does have one), yet no hind limbs.

-) Apes and humans have been famously connected by the study of genetics; in human DNA, there is a strand which is exactly identical to two specific segments of an ape's DNA. It appears to have been formed from two chromosomes that joined together at some point during our ancestry; this is made more readily apparent by the presence of two telomeres connecting together in the center of the strand --- normally, telomeres are only present at the end of a strand, but this particular strand is the length of two telomeres, indicating that they were likely two separate strands that had been joined together to form a single strand with an elongated telomere at the center.


One means by which a population can be speciated into two species (as in the above cases) is by mutation of the receptor-ligand complex that directs sperm to fuse with the egg; this is a "microevolutionary" step (a small mutation)  leading to a "macroevolutionary" event (the differentiation of species). This also, interestingly, appears to be an example of so-called "irreducible complexity" -- none of  the sperm will be able to fertilize the egg if the ligand on it (the egg) mutates, nor will they be able to fuse with the egg if their (the sperm's) receptor changes, and the chance that both will mutate simultaneously is not really worth considering. Thus, the populations with mutations rendering each other incompatible become "separate species," and the ones whose mutations match up become speciated thusly.

On a side note, speaking further of "microevolution vs. macroevolution"....interestingly, Answers In Genesis (a Creationist website which works to provide cue-card arguments for would-be hack debaters) includes this very argument as #2 on a list of  "Arguments that should be avoided (because further research is still needed, new research has invalided aspects of it, or biblical implications may discount it)." From AiG:

Arguments that should be avoided (because further research is still needed, new  research has invalided aspects of it, or biblical implications may discount it)

1. Evolution is just a theory. (“Theory” has a stronger meaning in scientific fields  than in general usage; it is better to say that evolution is just a hypothesis or one  model to explain the untestable past.)

2. Microevolution is true but not macroevolution. (People usually mean that we see changes within a kind but not between kinds; however, the important distinction is that we observe changes that do not increase the genetic information in an organism.)

Even their correction is wrong, however, because we do observe changes that do increase the genetic information in an organism. A single gene can "accidentally" reproduce itself twice, creating an extra copy, which then mutates separately from the original in future generations. This results in "new information" in  the genome that did not exist before the original mutation. One example of this (with which I'm sure Mr. McLatchie is familiar) is the hemoglobin of a human adult; without going into too much detail (again, Richard Dawkins has written about this one in The Blind Watchmaker, and about which he has also written about extensively elsewhere), there is evidence that the four protein chains in current human adult globins actually originated from an ancestor genome which "split" around 500,000,000 years ago into two parts; each part then later mutated separately and became a different cluster. This happened again around 400,000,000 years ago, and the alpha gene mutated again, following a similar path and giving us the zeta chain. This much is actually supported by contemporary phylogenetic analysis, as well --- other animals descended from those who existed around the time of the genome split (and which were associated with our ancestral line) also demonstrate this same split, and the same chromosomal arrangement of these genomes.

Gene duplications are not the only way to produce new information, however --- we also have events such as nucleotide insertions, as well as (possibly) viral manipulation. Basically, though, there are a multitude of ways to increase information in the genome through error or mutation.


Moving on to some of Mr. McLatchie's links, though, I'm curious about this statement (from a link provided by Mr. McLatchie to one of his own blog entries, "colliding with the pharyngula"):
At best, all his case demonstrated was common ancestry -- a proposition which is perfectly compatible with intelligent design.
....I have to say, I don't quite understand how he can say that common ancestry is "perfectly compatible" with intelligent design, yet without major evolutionary change. What he calls "macroevolution" is  commonly understood to be the primary vehicle for common ancestry! If common ancestry is demonstrable, but not by evolution, then by what method does he mean to imply that all life on earth evolved from a common ancestor? It seems mutually exclusive to say that all life we see today, in all its magnificent diversity, could have come from a common ancestor *without* major evolutionary change along the way. I'm interested in his explanation for this.

With regard to his "rebutall" of the popular rebuttal of Michael Behe's T3SS/bacterial flagellum argument....I'd like to refer to a couple of things: first, a study performed by students of the Department of Biology at the University of California at San Diego:

"[H]omologous flagellar proteins show phylogenetic clustering that suggests that the flagellar systems and Type III protein secretory systems diverged from each other following very early duplication of a gene cluster sharing many (but not all) genes.  Phylogenies of most or all of the flagellar proteins follow those of the source organisms  with little or no lateral gene transfer suggesting that homologous flagellar proteins are  true orthologues. We suggest that the flagellar apparatus was the evolutionary precursor  of Type III protein secretion systems."
--Phylogenetic analyses of the constituents of  Type III protein secretion systems (Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH  Jr.)
What the consensus tells us is that the flagellum and the T3SS probably each had an early precursor from which they diverged, which shared many (but not all) of the necessary genes to express the complete flagellum. As luck would have it, in his report (published in 2003 at Talkdesign.org), one Mr. N.J. Matzke lays out the following model of the evolution of the flagellum --- the method by which the flagellum moved from an early, primitive state to the so-called "irreducibly complex" flagellum we see today. Also take note, each of these steps involves the modification of only a single protein:

-) A simple passive pore exists within the membrane of a single bacterium, which allows  movement of proteins into the periplasm;

-) the association of a second protein makes the pore selective, allowing only specific proteins into the periplasm;

-) The F1F0 ATP Synthase associates with the pore, imparting active transport (Type III Export Apparatus);

-) Secretins and proteins, also ancestral to the flagellum, allow protein movement out of the cell. Association of a Secretin with the Type III Export Apparatus gives us the Type III Secretion Apparatus, which moves proteins from the cytoplasm to the extracellular environment;

-) An adhesive protein attempts to secrete, but becomes bound; repeating this process, proteins polymerize to form a pilus; as the pilus grows in length, the chance of finding a substrate to attach to increases;

-) Attachment of the pilus to the inner membrane increases its strength;

-) Wear/tear bends the pilus, allowing it to wiggle and thus further increasing the chance of finding a substrate;

-) The Tol-Pal system (which transports protons across a membrane) associates with the pilus, causing it to spin haphazardly, but thus allowing bacteria to escape crowded environments when nutrients are low;

-) Modification of the secretin releases any attachment between the former pilus and outer membrane; the remainder of the secretin becomes the P-ring, the former "chaperone' is modified into the F-ring --- both rings serve to stabilize the filament, allowing it to rotate freely;

-) Signal transduction proteins bind the proto-flagellum, linking its function to the state of the environment, thus forming a chemotactic flagellum.

For more of my thoughts on "irreducible complexity" and "specified complexity," you can go here. That's all I'm going to say about it in this article, though.


This is not a subject that's very easy to argue about; for one, the body of evidence that supports evolution is MASSIVE as it spans many topics (from biology to geology to geography to archeology to even astronomy). No matter where I choose to end this article, I'm going to feel like I still have much to say about evolution. But that's how these discussions work; no one person can hope to raise or rebut every possible argument for or against their position. I can only do my best to respond to the points made against me which I feel to be the most relevant and worth responding to. If I have failed to address anything very important, then feel free to leave a comment or snide remark or whatever below. Let it be known that I don't delete comments or anything, so have no fear of your argument being covered up. Although I reserve the right to ignore you or be a smartass if you try to pose as a "gotcha question" something which I have already addressed at length. Ask whatever you please but please don't waste my time! Thanks.

--Tim D.

Sunday, November 13, 2011

If You Can't Beat 'Em, Make 'Em Look Bad

As I have mentioned before, a few months back I was given the opportunity to write a guest post about evolutionary biology for the Evangelical Conservative Christian blog, Crossexamined.org. The idea was actually originally pitched to someone else --- after months and months of on-again-off-again debate about intelligent design and evolutionary biology, one of the other atheist commenters over there was challenged with the task of writing a short essay on evolutionary biology (specifically "macroevolution"), around 2000 words. The commenter declined, and I offered to do so in his stead. The blog host accepted, and although it took me much longer than I'd originally expected (due to personal drama and some unrelated business endeavors), I eventually managed to complete the paper and submit it, where it was promptly posted and where it still remains as of this posting. Shortly after, a Mr. John McLatchie submitted a response of his own to counter mine.

That is the simple version of that story. There's actually a little more to it than that; a couple of acquaintances and friends from various internet forums, with whom I'd shared the details of this situation as it developed, had warned me in advance that my posting would either be ignored, misunderstood/misinterpreted, or downright misrepresented. But I felt that, since I'd basically been given free reign to write in my own words, there was no way that my work could be misconstrued. And to a fault, I was correct. My work itself was not necessarily misconstrued --- no edits or alterations were made to the article, with one exception (the title, which I had wanted to be "What Is Evolution?", and which Mr. Turek seemed to have preferred as "Why I Think Macroevolution Is True." Not a big deal, really, so I didn't care much about that).

With this in mind, I made it very clear several times during Mr. Turek's and my exchanges that I was going to try to write on a more scientifically elementary level, given the quality of debates I'd had on CE.org in the past. Most of the frequent commenters there (with a few exceptions) seemed to have no real scientific background, and even less knowledge about evolutionary theory outside of that provided by various third-rate Christian propaganda pamphlets and programs and the like. Also, given my strict word limit, I figured it would be best to stick to the basics (so as to prevent long and detailed tangents).

So anyway, barring a few (rather long) delays, I was finally able to complete the article. I basically came to an impasse regarding the wordcount limit; given that the site was a Christian fundamentalist blog, I didn't want to clutter Mr. Turek's blog with a series of lengthy posts that most of his regular readership would probably not even give a second thought to; so I decided to try and put the gist of my argument into a single, compressed posting. I capped it at just under 3000 words, having torn and gutted out almost all of the real substance of the article even then (I am rather long-winded, but even after cutting out all my tangents and irrelevant points, it was still quite lengthy) and sent it off, along with a short note explaining that this was the best I could do, and that I would understand if they decided not to post it for me after all.

So after some brief (slightly awkward) discussion of the title, which I ultimately conceded, I sent him the article in full, which was posted either a few hours or a few days later (I don't recall exactly how long it took, but it was pretty quick all in all). I then received this email shortly after:

 ...which, having just submitted the final draft of my article, I found quite interesting. For if I had known that I would be "up against" someone with some professional background in biology, I would have written a very different article indeed! Given the word count under which I was operating, it would have been impossible to give a properly-worded response on a more detailed level, but I could have at least tried. Instead, what happened was that Mr. McLatchie was able to take advantage of my disadvantage, and focus on criticizing my arguments for being "elementary" and for "lacking evidence."

This is certainly the result of the fact that I was forced to remove many important examples in order to reach my desired word count (which, even then, I was stretching by almost threefold). This is not an easy subject to tackle in so few words! A more complete version of my original, uncut essay can be read here, and I will also be posting another rebuttal to Mr. McLatchie's counter-argument piece over on CE.org. Of course I will be posting it here instead of there, where it is significantly less likely to be viewed, but this is for two main reasons: (A) over here, I am free to write as many words as I please, and on my own schedule; and (B) I will be able to satisfy my aforementioned concerns with flooding a creationist website with scientific postings that will most likely go almost completely unnoticed (if you take a look at both posts on CE.org, you will see that there are almost no comments whatsoever besides my own and Mr. McLatchie's). At least here, I feel like it's in the right place, amongst other writings of similar nature. Over there, it just feels weird and out of place, I guess.

In any case, I have mixed feelings about how this all turned out....on the one hand, I was the one who made the conscious decision to take an elementary approach to this subject. So if I'm attacked for being elementary about it, I really do have myself to blame. And to be fair, Mr. Turek did offer me to post a series (instead of just one part) to complement my original article (which I ultimately declined because, although it would've been longer, with the word count per article limit, it still wouldn't have been enough). On the other hand, I can't help but feel just a *tad* bit slighted that Mr. Turek withheld from me that he would be submitting this for a more thorough rebuttal --- if I had known that, I would certainly have tried to argue from a different level. I had to waste so much time covering basics that I had almost no room left for the actual meat and potatoes of my arguments and evidence....if I had known that my primary rebuttal would come from someone who already knew all of that stuff, I could have used that valuable space to cover other more important arguments and ideas.

In the end, I guess I learned to be on my guard when discussing science with creationists....I can't help but feel that this was done with some degree of deliberate ill intent, perhaps to "weaken" my arguments and make them seem easier to rebut. I feel like giving myself a slap on the wrist for not listening to all of the friends and acquaintances who told me, in so many words, "it's a trap!"

I'd like to believe that the folks at CE.org are better than that, but after similar experiences (such as one of the other bloghosts' botched handling of an argument about intelligent design creationism, wherein he actively edited posts written by other users to cover up specific arguments made by those users), I have really begun to wonder if my faith in the appeal of reason to creationists is, perhaps, sorely misguided.

--Tim D.