Wednesday, February 8, 2012

Reducible Complexity: reply to the IDeologs

The gaggle that continue to raid evolutionary biology blogs, patrolling for things that can be naively or intentionally misinterpreted as evidence for their theological views, specifically 'Intelligent Design' (ID), loves to concentrate on complex traits.  They claim such traits cannot have evolved because the independent components won't function on their own and the whole breaks down without them.  They call that Irreducible Complexity:  since you can't take any components of complex traits away and still be viable, such traits could not have arisen gradually by natural selection.  Therefore (the IDeologs say), Intelligent Design is true.  But this is false on several grounds, not all of them even recognized by biologists, who often defend evolution by needlessly agreeing to do it on the IDeologs' turf.

First, it is IDiotic to argue that if an evolutionary claim is false, therefore creationism is true.  That is simply a logical fallacy.  If evolution as biologists see it were being misperceived, that in no way provides evidence for any specific counter explanation.  Only an IDeolog would make such an argument.  It would be just as sensible--that is, as nonsensical--to say that our misperception proved that life came to earth from a parallel universe in a spaceship made of banana peels.  We get things wrong or understand them incompletely in evolutionary biology, which is why it remains an active science, but that is not evidence that evolution didn't happen.

Second, the major IDiotic argument about the need for completeness was one Darwin was aware of and even speculated on in regard to the eye, a favorite irreducible complexity example cited from that time to the present day.  Darwin suggested ways that primitive light sensitivity could have evolved bit by bit.  In what was really striking prescience, his basic speculations have been shown to be about right, because species alive today with 'partial' vision have been found, and genetic components of vision are shared among species with simple as well as complex light reception.  Even saying 'partial' vision is a subtle misnomer, because each species uses what it has: the light sensitivity of a worm or bacterium is not partial for their uses, and to use the adjective suggests the IDiological view that humans are at an intended pinnacle, that our vision is somehow more complete or real than a clam's.  That's an egocentric misperception of evolution.

Complexity is reducible!  It always has been.  It's a central aspect of life.   Right here and now
Thirdly, and perhaps even more important than the first two reasons why the anti-evolutionary IDeology is just plain wrong is that complexity is typically reducible!  The basic IDeologs' premise doesn't have to be refuted because it's not true.

What we know very well is that most traits of organisms are, in fact, the result of multiple interacting factors (gene networks, the  polymeric, cooperative nature of DNA and proteins, signaling and receptors systems, gene regulation, and multipart proteins, etc.).  And, eyes, too.  That is a central fact, and a main point of MT (the blog and the book).  We know from thousands of studies (yes, even the GWAS and other 'omics' studies whose excesses we love to point out) that complex traits really are complex at the gene level.

The same studies also show by their very nature--by the very fact that we are doing so many of them in the first place--that each person will have a different genotype, a different set of variants, involved--even if they have the 'same' trait, like stature, insulin levels, blood pressure, or behavior.  That is why personalized genetic medicine is unlikely to work nearly as well as advertised.  Personalized medicine almost assumes irreducible complexity: enumerate the parts and then any variation in the trait must be due to a broken part that can be identified.  But that isn't how Nature works.

Reducible complexity is true even of vision: Color-blind people are people and they have vision, yet they are missing functional light-sensitive genes (e.g., genes that are used in red or green detection, or overall light sensitivity). Visual acuity varies in all sorts of ways among perfectly viable people.

This is typical of biological traits.  And recent studies have clearly shown that each of us is walking around with numerous completely inactivated genes, whose 'damaged' sequence variants we have inherited--from parents who somehow had managed without them.  One recent paper found that around 165 different genes were completely inactivated (both copies not working) in a typical person.  And there are many others in which one of our two copies is not working normally.  The combination of inactive genes would be different for each person, but the truth is that we do not normally need all the genes in our genome.  That tolerance of variation is exactly the working material that biologists have known is at the basis for evolution from Darwin's own time.

Confirming this in another way, and also very clearly, is that it is routine that a gene experimentally inactivated in a laboratory animal, like a mouse, has serious effects in some strains but little or even no effect in others. A mutation causing a serious disease in humans may do nothing when the same mutation is tested in a mouse, or it may have similarly bad effects only in some strains.  That's one of the notorious problems with mouse models for human traits: mice and people share many traits but we make them differently to various extents. There is more than one way to make the same trait.  Complexity is reducible.

The reducibility of a trait, to put it in terms even an IDeolog could understand, depends on the combination of genes being viable, not on every gene having the most functionally efficient variants.  The importance of component cooperation, a favorite MT word, is in part that various types of cooperation are viable.  That aspect of redundancy and variation is one of the central reasons that complexity could evolve in the first place, exactly in the general fashion argued by Darwin and since.  No biologist suggests that an eye just emerged wholesale from the primeval slime.

But there's more.  Studies of the nature and evolution of genomes shows very clearly that genetic mechanisms arise largely by means that generate redundancy as well as alternative pathways to given outcomes, as cells respond to their local environment.  Gene duplication occasionally leads to individuals with two copies of a gene where in their ancestors there was only one (this happens in species generally, not particular to humans in any way).  That can provide redundancy, so that one of the copies can acquire mutations that alter what the gene does, while the other copy keeps plugging along with the original function.  The new function can be due to mutations in the  protein code of one of the copies, or the DNA sequences that regulate when and where the gene is used.

For these reasons, traits are the result of many different genetic contributions, all varying among individuals, each reaching similarly viable traits with different combinations of that variation.  Those combinations that aren't functional don't survive or reproduce; those that have an advantage may do better.  Over time, the mix of variation, including even the number and set of contributing genes, allow traits to evolve new or altered function.

This is how evolution works, gradually producing new or varied traits.  We understand this because we are aware that complexity is often, or even typically, reducible.  Although it hasn't been put this way before to our knowledge, this is nothing more than a modern understanding of classical evolutionary ideas.

The IDeologs claim that reduced complexity could not have existed in a stepwise, bit by bit, assembly of a new trait from parts that would not work on their own--that evolution couldn't get from there to here. But the deeper truth is that evolution is both there ('incomplete') and here ('complete') today and has been that way at any or even every time in the past.   It isn't just that things have to be assembled over time by different steps, but that they exist at any given time in various steps or stages of 'completeness.'  To a great extent, biological complexity is  inherently reducible at any time as well as over time.

And one more reason:  Of course, we needn't have gone through all of this to convince you that complexity was reducible, after all.  That is because the IDeologs disprove their own irreducibility argument by their very existence:  one can function as a human being even with a brain that allows you intentionally not to use it to recognize the realities of the world--by not using the thinking complexity they were born with!  We would apply this to those who lead the movement, and do or should know better, but not those who they naively lure into adopting its know-nothing IDeology.

Finally, we may make sport of intentionally or willfully self-deluded critics of evolution.  For any of those who are sincere but naive, one can only say that it's too bad, and poignant, too, that science shows the evolutionary nature of life, rather than the comforting existence of a benign divinity who graced the earth with our presence.  How nice if that could be true!  How hard it makes it to understand the injustices and suffering in the world.  But science is about the real world, not the one we might wish for.


Hollis said...

Thanks for another great post -- well-articulated responses to the IDers. But IDers ears are deaf to this kind of information. I sometimes wonder if it isn’t more useful to critique rather than to defend. It would be easy to do; faith-based creationism and ID are basically mythology.

But who wants to bother figuring out the details of their stories! And unfortunately, in the human mind opinion often comes first and “evidence” is then gathered to support it. Conservatives tend to be more fearful, and fear can reinforce this behavior. I bet it’s comforting to have a simple world view!

Jonah Lehrer on human “reasoning”:
“So here’s my new metaphor for human reason: our rational faculty isn’t a scientist – it’s a talk radio host. That voice in your head spewing out eloquent reasons to do this or do that doesn’t actually know what’s going on, and it’s not particularly adept at getting you nearer to reality. Instead, it only cares about finding reasons that sound good, even if the reasons are actually irrelevant or false.”

fear and political views:

Ken Weiss said...

Well, it's certainly true that IDers are deaf to the information (often intentionally, I think). But while I agree that faith-based claims are outside the realm of science, and without any scientific support that I know of, they aren't really 'mythology'. To those with strong beliefs, they are simply a different kind of truth and reality.

As to who wants to bother, when nearly half the country not only accepts religious-experience as a form of truth, but also denies the material evidence for evolution, I think one needs to keep asserting the strength of the evidence for evolution--while fully acknowledging that science is about trying to figure out those aspects of it that we don't yet understand.

I would not want to try to refute ID, but this post was intended simply to say that there is nothing to refute, since complexity is demonstrably reducible in the here-and-now.

I won't dispute the fear element, if you mean in this case the extension of fearful predisposition to fear of death and yearning for eventual justice.

Thanks for the links and quote. Economists have (for the moment) started to accept that 'rational' is as rational does. For most of us, probably, rationality ends when self-interest begins, or something like that.

Oh, to be a gnat, without knowledge that soon a bird or bat will come along and this wonderful world will just disappear. Of course, it was how not-so-wonderful it is that Darwin found so moving.

James Goetz said...

I remember when I thought that Behe was on to something constructive. I recall an interview where another scientist pointed out that one of his articles missed important counter data in the academic literature. Behe replied that his choice of search terms did not bring up those articles. I recalling feeling confident that Behe would then meticulously work on following up of all old and new research related to his proposed cases of irreducible complexity. Hmm, that never happened with a single case.

Ken Weiss said...

It's too bad, because bad science distracts from the important aspects of religion, the value of accepting something 'on faith' (which can be edifying, if it is not necessary for it to be factual in the usual material sense).

We have many mysteries about Nature yet to understand. Dark matter and parallel universe ideas, perhaps string theory, indicate that. We don't know how our understanding will come out, or when.

Whether or what form any kind of 'higher power' will be found, it is unlikely to be the kind of personal deity that sacred texts proclaim, because that deity could have provided more materially consistent truths.

But whether any higher power, or higher level of organization, whatever it may be (if anything) provides comfort and edification, is one of the important questions. It's been asked by thinkers, poets, scientists, mystics, and just plain folks since time immemorial.

Each must find his/her own answer. But intentionally sloppy claims about the material world, like Behe's, do a great disservice to those who are seeking truly to understand life, what it means, and how to live it.

James Goetz said...

Ken, I agree with your above paragraphs one, two, four, and five, but I'm unsure of what you mean in paragraph three. In any case, the scientific method will never find any deity. But when you say that it's unlikely that there's a personal deity as taught in say sacred Christian texts, then I disagree with you. However, there are various interpretations of the texts that I reject. Also, I'm unsure what you mean when you say, "That deity could have provided more materially consistent truths."

Does that mean the the deity could have left material evidence that unequivocally points to his existence?

Or are you making a statement about inconsistent truths in the sacred texts?

Or something else?

Yes, this is going off the original post, but you started in that direction. : -)

Ken Weiss said...

Well, I don't see how science can show that there is a 'personal' deity of the kind envisioned by sacred texts. In that sense, there isn't any material evidence for such a deity. So in what way can you say it is 'likely' that such an entity exists?

If faith or experience with personal communication is evidence, then for whatever reason only some people experience the evidence.

If the deity wanted fealty, He (if that's an appropriate term) could have made it plain and clear that He exists and soon. Ambiguous counter-factual scriptures don't help, if one takes a scientific view about the material world.

I'm saying nothing new. Either we're the 'salt of the earth' literally, or there is room for interpreation. If the latter, than there is no way to get what would count as a scientific explanation, since the facts as stated don't fit material reality.

I personally would love to be the scientist who could prove the existence of a benign deity, of an afterlife, and so on. But I don't see the evidence, and if we're not to ask for evidence, then it's hard to know where to turn except to personal subjective judgment about what life and how to live it.

James Goetz said...

You bring up many important points. There's enough concepts in this topic to write an entire book or more about it, which I hope to do in the future. In short, to begin with, I reject scientific explanations or any "proofs" of God while some scientific discoveries can add support to philosophical "conjectures" of a personal creator of the spacetime continuum (God) who has a long-term plan for reconciling with all humans.

You ask, "So in what way can you say it is 'likely' that such an entity exists?"

A good starting point with conjecturing the "likeliness" of a personal Creator of the spacetime continuum involves analyzing the beginning of time, which involves a debate that goes back to the sixth century AD. This is a type of cosmological argument that is typically presented as a formal proof such as William Lane Craig's kalam cosmological argument, but I reject formal proofs of God and use similar concepts to defend a reasonable conjecture of God, for example, my blog article "First Quasi-Cause: Uncaused Timeless Nature." And if you think that I made a reasonable conjecture of an originally dimensionless personal Creator with that article, then opens many more questions that would take at least one book to cover, especially for nonbelievers.

On the more existentialist end of my conjecture is my believe that I enjoy a personal relationship with God.

Ken Weiss said...

Far be it from us to attempt to dissuade anyone from what they have personally experienced! The idea of deism or theism, that there is a God who started it all is, of course, ancient. But that doesn't come with any evidence other than it is easy to imagine it and hard to imagine there being no existence of any kind etc., or to imagine how the universe could be.

But that's a far cry from the idea of a personal God who, in the vastness of the same universe would care about us measly blobs of protoplasm. Or one who would tolerate, much less be responsible for, the cruelty and injustice, a full share of which is done by believers.

Anyway, I'll certainly want to read your book! I know you have been giving very thoughtful attention to these subjects for many years. If I had any kind of personal experience that convinced me, or that I could not just as easily attribute to illusion, of course I'd be very happy.

But none of it would relate to the topic du jour, the false reasoning of IDers, and the little appreciated fact that there isn't any particular need for evolutionary explanations of 'partial' traits because Complexity is clearly reducible even in our own time, so obviously isn't a problem over evolutionary time.

James Goetz said...

Thank you. I'm excited to get my first book under my belt.

Back to the main topic, perhaps Behe could make some cases for unlikely complex molecular tinkering, but he has no case for the intelligent design of irreducibly complex biochemical systems.

Ken Weiss said...

There is of course the point that one may call arrogance or presumptuousness on our part even to use the word 'intelligent', or try to infer about that, in the context of a God who is widely believed to be omniscient, omnipresent, and omnipotent. Presumably God is smarter and less superficially crude than humans are, and why would we even expect God's thinking processes--if the word 'thinking' even applies--to resemble ours in any way at all.

And we cannot be in any God's image and likeness given that we are so far from omniscient, omnipresent, or omnipotent.

James Goetz said...


In all fairness to the leading ID advocates, they say that they have yet to identify the intelligent designer. For example, Behe says that possible candidates for the intelligent designer of bacterial flagella include (1) God Almighty, (2) God who died after designing the flagella, or (3) an alien who left no other material evidence except the irreducibly complex bacterial flagella. Hmm, I suppose that Behe also needs to consider if the intelligent designer of blood clotting was a different designer than the intelligent designer of the blood clotting cascade. After all, the blood clotting cascade sometimes fights off various potentially deadly flagella attacks. : -)

Concerning your comments about religious texts stating that humans are made in the image of God, there are lengthy philosophical discussions that explore what that means and does not mean.

James Goetz said...

sorry for typo:
Hmm, I suppose that Behe also needs to consider if the intelligent designer of [flagella] was a different designer than the intelligent designer of the blood clotting cascade. After all, the blood clotting cascade sometimes fights off various potentially deadly flagella attacks. : -)