What If We Played Chess the Way People Argue?

Throughout the years, I have noticed a pattern that occurs when arguing with various people on the internet – rather than focus and deal with the actual argument I am making, they are arguing against a point that they anticipate I will make later down the line. Rather than address the question I am asking, they address the answer they think I am trying to elicit.  To argue and respond like this, I assume they think they are playing mental chess, relying on their clever foresight to anticipate my next move.  But more often than not, they are simply relying on their own stereotypes. So what would it be like to play real chess with someone like that?

Turner and Evolution

I just finished reading an interesting paper by J. Scott Turner from the Department of Environmental & Forest Biology, SUNY College of Environmental Science & Forestry (Extended Phenotypes and Extended Organisms. Biology and Philosophy 19: 327–352, 2004).  Turner raises several arguments that I find to be quite friendly to the Design Matrix. But what stood out the most was this:

The gene’s special nature derives not from its ability to encode function, or to replicate, or to accumulate mutations, but from its longevity as a determinant of future functional environments. Put simply, of all the multifarious influences that could be brought to bear on the specifiers of a living environment, the information encoded in genes simply outlasts any others (Figure 8). Specifiers and epigenetic effects on them come and go. Genes endure and evolve.

When you consider all the debates about genes and function, what has been missing is consideration of this special property of all genes – their longevity as a determinant of future functional environments.  Genes, which can be considered a core component of life’s internal architecture, are perfectly suited to carry out the function of evolution.  And even if it is the case the geochemistry ultimately spawned genes, this fact would force us to consider that geochemistry did not come up with an alternative for genes.  There are no living things that exist without genes.

But it gets better.

Need Some Air

Back on May 19th, I wrote:

Oxygen is a biological output that, in turn, creates a new context to elicit further changes. Rising levels of oxygen are correlated to the two most radical transformations in evolution – the origin of eukarya and the origin of metazoa. There is no reason to think something as complex as the eukaryotic cell, or the metazoan body plan, would have emerged without oxygen.

A month later, a study came out that supports this line of thinking:

Pick a Number

Economist Rob Hanson quoted Tyler Cowen from George Mason University:

We often like to ask lunch visitors what is their most absurd view (in the eyes of others). Alas I have so many choices. On BloggingHeads, Tyler Cowen answers this for Will Wilkinson:

Tyler: My most absurd belief, perhaps, is the extent to which I think people should be truly uncertain about almost all of their beliefs. And it doesn’t sound absurd when you say it but I don’t on the other hand know anyone who agrees with it. … Take whatever your political beliefs happen to be. Obviously the view you hold you think is most likely to be true, but I think you should give that something like 60-40, whereas in reality most people will give it 95 to 5 or 99 to 1 in terms of probability that it is correct. Or if you ask people what is the chance this view of yours is wrong, very few people are willing to assign it any number at all. Or if you ask people who believe in God or are atheists, what’s the chance you’re wrong – I’ve asked atheists what’s the chance you’re wrong and they’ll say something like a trillion to one, and that to me is absurd, that even if you think all of the strongest arguments for atheism are correct, your estimate that atheism is in fact the correct point of view shouldn’t be that high, maybe you know 90-10 or 95 to 5, at most. So that maybe is my most absurd view. Most things are much more up for grabs than we like to say they are.

Will: I agree with you that things are more up for grabs than people think they are, but I have real problems with the idea that it’s either possible or desirable that people assign probabilities to all of their beliefs. I think it’s a weird violation of the actual computational constraints of the human mind, that we just don’t.

Tyler: Here, you are more of a philosopher than I am, and I’m more a Bayesian. I’m sure it’s possible. Now I’m not saying it’s desirable, I’m just saying I want people to do it in a lot of instances, maybe just for my aesthetic pleasure. I want to pin people down and get a sense for how sure they are, and interpret these probabilities as betting odds, if you want. Let’s say there’s a lot of dying starving children in India or sub-Saharan Africa, and you are offered to bet, and you know that the money won on these bets will go to feed these children and save their lives, and you have to name what odds you are going to bet at. And you can name a number. You want to name the best number you can because you want to save the lives of these children, so I’m not going to allow any evasion here. I don’t see why there is not always some pick of a number that’s better than a lot of other picks. You are not going to get it right so computationally of course it’s hopeless. But look, you’ve got to give it your best guess. (emphasis added)

Evolutionary capacitance

Previously, I took issue with John Avise’s abrupt description of alternative splicing as having “some advantage,” as alternative splicing may play a crucial role in the evolution of metazoans by shielding sequence from selection, allowing minor variants to emerge and grow before being put to the full test of selection. It’s such shielding that might be required to expand a more complex state. One way to think of alternative splicing is as an evolutionary capacitor. I’ll let the Masel group describe what that means:

An Interesting Endorsement

One person with a doctorate in religion and science and two well-reviewed academic books on science and creation doctrine observed:

Nonetheless, I would say that Mike Gene has come closer than any other human being (and far, far closer than any of the famous TEs) to convincing me that it just *might* be possible to reconcile pure neo-Darwinism with orthodox Christian theology.  Whereas all the other TEs come up with arguments that to my mind are just sophistry concealing blatant contradictions or muddy thinking, Mike has a radically different approach.  So if someone wants an argument that just might be able to justify baptizing Darwin, Mike’s your guy.

Alternative Splicing and Evolution

Let me add one more comment concerning Avise’s PNAS paper.  In the last entry, I focused on his argument that introns counts as evidence against intelligent design.  We saw the whole argument fails if we envision design working through evolution.  But I want to you to notice something else.  In the paragraph preceding the discussion of introns, Avise wrote:

Approximately 1% of all known genes in the human genome encode molecular products that our cells employ to build spliceosomes and conduct splicing operations on premRNA. All this rigmarole has some advantages (e.g., opportunities for alternative splicing during ontogeny and exon shuffling during evolution, both of which can generate functional protein diversity), but such benefits do not come without major fitness costs.

Note that Avise describes alternative splicing as something that confers “some advantage.”  Some advantage.  As if alternative splicing is just a minor factor in evolution.

Now let’s contrast this to the abstract from a paper by Stephanie Boue, Ivica Letunic, and Peer Bork  (Alternative splicing and evolution. BioEssays 2003 25:1031–1034):

Alternative splicing is a critical post-transcriptional event leading to an increase in the transcriptome diversity. Recent bioinformatics studies revealed a high frequency of alternative splicing. Although the extent of AS conservation among mammals is still being discussed, it has been argued that major forms of alternatively spliced transcripts are much better conserved than minor forms.(1) It suggests that alternative splicing plays a major role in genome evolution allowing new exons to evolve with less constraint.

“A major role in genome evolution” sounds a tad more than “some advantage “ to me.  In fact, consider the conclusion of Boue et al.:

Fallout from a False Dichotomy

So what is the consequence of Avise’s false dichotomy?  The bulk of his paper is a detailed exploration of the “outlandish features of the human genome that defy notions of ID by a caring cognitive agent.”  While this is an argument that works against design that is coupled to special creation, it fails against design that is coupled to evolution.  To see this, let’s pick one of the outlandish features that Avise explores – introns. I chose this example simply because I have already written about it.

Avise’s core argument is as follows:

There are good reasons to think that cells might be better off without introns, in an ideal world.

Let me now add to this argument with the following point:

There are good reasons to think that evolution might be worse off without introns.

In other words, if introns are an “outlandish features of the human genome,” we might also point out that without this outlandish feature, there is no evidence to think that evolution would have cobbled together a human, or human-like, genome.

Recall that I have used the teleological perspective of front-loading to propose a testable hypothesis about introns – they have facilitated the emergence of metazoan-type complexity – that is supported by evidence (here, here, here, and here) and has been successfully defended.  (If you have not read these essays, then what follows below will not make much sense to you).

If the design objective is to nudge the emergence of metazoan-type complexity, and not to ensure that cells would be “better off,” then we can see that Avise’s core argument has collapsed.

Nevertheless, let’s have a look at Avise’s reasons.

The False Dichotomy

In the last entry, we saw that biologist John Avise argues that traits which are gratuitously complicated, function poorly, and debilitate their bearers, all count as evidence against design.  And as I noted, I agree with this assessment.  In fact, Avise is unknowingly participating in one facet of the Design Matrix – the criterion of rationality.  What’s missing from his argument are two things: 1) Assign a numerical score to better nail down and communicate this judgment of irrational design and 2) An acknowledgement that a fair-minded and open-ended analysis would have to include the willingness to score things in the other direction, such that traits which are not gratuitously complicated, function exceedingly well, and do not debilitate their bearers, count as evidence for design.  To argue otherwise would be to engage in apologetics.

But there is a more fundamental problem with Avise’s argument.

The Other Side of the Coin

Biologist John Avise recently published a paper about intelligent design in the journal PNAS entitled, “Footprints of nonsentient design inside the human genome.” Avise poses an argument against ID:

my focus in this paper is on a relatively neglected category of argument against ID and in favor of evolution: the argument from imperfection, as applied to the human genome in this case.

The problem here is that Avise never defines or describes perfection. So how are we to determine if imperfection exists? What’s more, Avise never makes the case that intelligent designs must necessarily be perfect designs. Given these two simple facts – failure to define perfection and failure to show that design entails perfection – Avise’s stated focus fails.

But the situation becomes much more interesting if we simply discard the focus “on imperfection” and consider what Avise is trying to communicate. I think this portion of the abstract makes his argument more clear:

Yet, many complex biological traits are gratuitously complicated, function poorly, and debilitate their bearers.

It’s not that some system or feature is “imperfect” that is relevant. It’s that the system or feature is “gratuitously complicated, function poorly, and debilitate their bearers.” For any system that is indeed gratuitously complicated, functions poorly, and debilitates their bearers, is not something I would consider to be intelligently designed. This is even more true if the poor function and constant breakdowns are a consequence of a complexity that is gratuitous. If I had reviewed Avise’s paper, I would have suggested he drop the whole “imperfection” argument and focus on first establishing the gratuitous nature of biotic complexity and then tracing poor performance to this very gratuity. I think that is the argument Avise is making, but it gets lost in all the harping about imperfections.

As you know, I do agree with Avise that such “bad design” counts as evidence against intelligent design. Otherwise, why label a design as being “intelligent?” But I also believe in a fair- and open-minded approach to these issues. Thus, I would follow through with Avise’s logic to the next step.