Why is the "black box" so complicated??

I received an e-mail question about a recent article I wrote with a graduate student. The question shows a common misunderstanding of evolution, and I thought it would be interesting, or at least potentially useful to more that one person, to post my response here.

Hi Dr. Oakley,

I am writing a research paper and came across your paper entitled, Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution. I was hoping you could give me your perspective on a question that is part of my research interest.

Since a simpler mechanisms for phototransduction would theoretically work, why would evolution favor a more complicated phototransduction cascade with intermediates such as transducin and PDE? I would greatly appreciate any insight you could provide me.

The implication in the e-mail is that evolution is a force that produces sleek perfection. Expensive solutions to problems should not arise by evolution (or at least they should not be maintained), especially if the complexity is unnecessary. This is a modernist view of biology, a view that can be found in 20th Century biological research, and a view that is also common today among students, and the general public outside the field of evolutionary biology. It is a view that results from an often unstated assumption natural selection is a supremely powerful force that leads to perfection.

From this Modernist, Bauhaus perspective, it is indeed perplexing to learn that opsin initiates a complex, baroque, Rube Golddberg-like cascade to turn light energy into a nervous impulse. This cascade includes reactions from opsin->transducin->PDE->CNG; each protein signaling in one way or another to another protein down the line - and this description is even VERY simplified compared to the actual complexity!

So the question is, why would evolution "favor this complicated phototransduction cascade", when all that seems to matter is that opsin signal directly to the CNG ion channel protein to cause the nervous impulse.

The most direct answer is that evolution is not an Intelligent Designer, rather it is a bricoleur, a tinkerer. Evolution acts upon what is available, and things that are useful are kept. In the case of the phototransduction cascade, evolution co-opted existing components: an existing GPCR cascade gained light sensitivity. We know this because the components of phototransduction pre-date opsin (e.g. here). Phototransduction was not invented from scratch, in the most efficient way possible. Instead, it was cobbled together using available parts.

This can be conceived as an example of a phylogenetic or historical constraint. In other words, history matters. All living things and all components of living things share a common history. Because of this, and because of the interdependence of components of living things, it is usually not easy to completely re-invent something. The number of shared genes in all animals (for example) clearly illustrates that history matters. Components are used and re-used, not invented anew.

This answers the proximate question, of why phototransduction is so complex. But doesn't address the question of why all GPCR cascades are so complex. I don't know the answer to this, but perhaps the complexity allows for flexibility. In fact, GPCR cascades are supremely flexible, and underlie signaling from outside to inside cells for many processes in animals, including vision and other senses, hormone signaling, metabolism, development, reproduction, etc, etc.


Interestingly, this question showed me yet another new perspective on the flawed argument for Intelligent Design. ID proponents suggest that when we see something outlandishly complex, then it must have been designed by an intelligent agent. However, as this question points out, extravagant complexity is not a sign of intelligence. Why use 50 components when 2 will suffice? Elegant simplicity is far more intelligent than excessive complexity. Again, evolutionary biology provides a logical and plausible explanation for the biological processes that we are coming to understand.

Dispatch from the front lines of Ray Comfort's Krazee crusade

The "special" 150th anniversary edition of Origin of Species - the one with 59 pages of anti-scientific banana mush as an introduction - was handed out at UC-Santa Barbara on Thursday. Word on the street was that a number of campuses were hit on Wednesday, and by ~10:30am on Thursday, we at UCSB were starting to feel somehow let down, like we wouldn't get our chance to see the circus, and maybe just a little like a wallflower at the junior high dance.

Then the news hit. Graduate student Sabrina poked her head into my office around 11 and asked if I was ready. I was. Mostly I wanted my souvenir. Graduate student Chris Evelyn was already on the scene. Chris is an evolutionist with a strong competitive streak, and he was not about to let Ray Comfort's propaganda be distributed freely. Chris had found two people handing out the books near our library, and he contacted Sabrina, who let me know. I rattled off an e-mail to our Biology email list, and headed off to battle.

Aside from people paying to throw pies in the face of frat boys (fund raiser), demonstrations to save ESS (UCSB's exercise department is getting cut), flyers from "Jews for Jesus" (sounded interesting, but I didn't get one), and some other activity and demonstrations around the library (Free Palestine!), I saw no copies of the Origin, and no sign of Chris or Sabrina.

"We're over at the UCEN", Sabrina sent me a text. I walked 5 minutes over to the University Center. It was another fine Santa Barbara day, crystal clear blue skies, 70 degrees, and crisp shadows from the intense sunlight. The Comfort-ites, two of them, had run out of books. They had each carried a backpack-full to near the library, where Chris had found them. Now they were making plans to get more books. They had to park in Isla Vista, a 15-20 minute walk from the library. Chris followed them to their van - he didn't want a single book to be handed out without an NCSE flyer. Sabrina and I went back by the library to wait for the return.

By that time, my email had hit the biology department. About 10-15 other biologist found us and together we waited for the return of the banana editions. Independent of us, an Undergraduate Skeptics group called SURE was on the scene. They were prepared with flyers from Don't Diss Darwin and had written a counter argument to Comfort's banana-mush preface. Chris, still following the distributors, kept us updated by text messages. "They have hundreds of books in a van!"

Finally, they arrived, and I got my copy. I talked a bit to one of the distributors. "Jason" had a full red beard and wore a baseball cap. I learned he lives in Ojai, and he's 35 and unemployed. He had a calm demeanor, and he didn't know what he was getting into. He had recently joined a bible study group, and his friend "Mike" asked him to help pass out some books. He did not expect any sort of confrontation at all, and went out of his way to make clear that he didn't really know about what was in the book. He'd hand out a book and say things like "make sure you get a flyer and see the other side of the argument".

The other distributor, "Mike" was a older than Jason, maybe 60. He was a bit more evasive, and for a while seemed to want to get away from the skeptics and the biologists. I didn't get a chance to talk to Mike myself, but I learned that he was a veteran of military service. After a while, he too was telling people to get our flyers, to be fair. Poor Mike - most everyone I saw was a biologist just trying to get one of these laughable souvenirs. Poor Jason - he was just helping out a new friend, handing out some books.

We invited Jason and Mike to come to our screening of "Judgment Day: Intelligent Design on Trial". They declined. Their goal was to hand out all the books. Chris made sure flyers were present, and the Skeptics were troopers, too, sticking with the distributors through the evening; although several came to the screening.

After the screening, I got another text from Sabrina "Debating going on near the library". I already had plans to take my kids to the UCSB soccer game, first round of the NCAA tourney (we won, 1-0). Chris and Sabrina, and probably Nathan, were fighting the good fight though, and I think almost no books were handed out without a flyer or NCSE banana-bookmark, or both, as accompaniments.



A little activism was fun, and I was proud that evolutionism and rationalism had a much stronger presence than anti-science banana-mush. Although this sort of thing can be energizing, in the end, I mostly feel bad for Mike and Jason. This feeling was echoed by an email I got just now from Chris.

Chris thinks that, in the end, all this was just a cheap scam perpetrated by Ray Comfort. We found out that Mike put up money to buy these books. Comfort wrote a bunch of crap, tagged it to the beginning of Darwin's classic, published cheap copies, and then used his propaganda machine to get gullible buyers to spend their money.

I shouldn't be surprised. This to me is the lowest point of religion: the fact that (somehow) charismatic, yet underhanded people seem always to be able to lighten people's wallets in the name of religion. It's happened for centuries. Still, seeing it in action, and meeting the victims, makes me feel completely empty. I'm reminded of a time when I visited New York City and street con artists pulled cash right out of the hand of my friend. The rest of the trip was not the same. It seems to me that Ray Comfort is no better than one of these street con-artists. Perhaps it would've been more fun to be at UCLA, where Ray himself was, instead of witnessing his victims gradually realize they were caught in a scam.

10 Great advances in evolution-Nova Beta

pbs.org has a new format for their web-based information on Evolution. There is a lot of great information there. Here is an article by Carl Zimmer entitled "Ten Great Advances in Evolution", which draws upon similar material to his new textbook.

Conference and Blog contest

Dear Colleagues,

Apologies if you have already received notice of this opportunity.

It is my great pleasure to announce that the National Evolutionary Synthesis Center (NESCENT) in Durham will be funding 2 travel awards for Science Online 2010 in Research Triangle Park, NC. This annual (un)conference (http://www.scienceonline2010.com/index.php/wiki/) to "explore science on the web" takes place January 15-17 and is free to attend. Two awards for $750 each are meant to offset the costs of participating in the conference and are open to anyone from any country. To qualify, you need to write a blog post about evolutionary research that was published in 2009!

"To apply for an award, writers should submit a blog post that highlights current or emerging evolutionary research. In order to be valid, posts must deal with scientific results appearing in 2009. Posts should be 750‐1500 words, and must mention the NESCent contest."

For more details: http://deepseanews.com/2009/09/travel-awards-for-scienceonline-2010/

Please spread the word on your own blogs, tweets, webpages, news blurbs ,etc. It is great for such a prestigious organization to support online science communication in this way!

Refuting Comfort's Eye evolution claims

As I mentioned in my last post, Comfort and Cameron will be distributing co-opted copies of Darwin's ...Origin... I've looked at the introduction Comfort wrote. Of course it contains the same old tired anti-evolutionist arguments that have not changed in hundreds of years, despite the fact the field of evolutionary biology has matured into a rich, detailed, predictive science that forms the core of modern understanding of all biology.

[If you don't read the entire rather long post, please read the last 2 paragraphs]

A prime reason evolutionists don't often debate these simplistic claims is that it's been done before, for hundreds of years, and anti-evolutionists keep re-using the same tired arguments, ignoring advances in science. Scientists really like to argue, but not about things that have been resolved for hundreds of years, over and over again, in increasing detail.

Comfort's simplistic, tired arguments are no exception. I'll focus on his section on eye evolution. The arguments boil down to:

1. It looks soooo complex. It had to be designed.
2. Comfort can't imagine how "random" processes could drive evolution.
3. There are a bunch of parts working together, and each couldn't originate without the other.

Of course there is nothing new here. For #1, Hume famously critiqued the design argument in the 1700's. It part, this is a false analogy: Watch is to human designer as Complex biological feature is to God.

#2 Natural selection is not a random process, e.g. Blind Watchmaker.
#3 There is no evidence that "separate" parts of the visual system cannot work separately, and in fact it is known that parts DO function separately. As one of many possible examples, the cnidarian polyp Hydra magnipappillata uses photosensitivity without eyes or brain (ref).

Below, I will paste Comfort's text, and a few comments on his text.

Or, consider the human eye. Man has never developed a
camera lens anywhere near the inconceivable intricacy of the
human eye. The human eye is an amazing interrelated system of
about forty individual subsystems, including the retina, pupil,
iris, cornea, lens, and optic nerve. It has more to it than just
the 137 million light-sensitive special cells that send messages
to the unbelievably complex brain. About 130 million of these
cells look like tiny rods, and they handle the black and white
vision. The other seven million are cone shaped and allow us
to see in color. The retina cells receive light impressions, which
are then translated into electric pulses and sent directly to the
brain through the optic nerve.

A special section of the brain called the visual cortex
interprets the pulses as color, contrast, depth, etc., which then
allows us to see “pictures” of our world. Incredibly, the eye,
optic nerve, and visual cortex are totally separate and distinct
subsystems. Yet together they capture, deliver, and interpret
up to 1.5 million pulse messages per millisecond! Think
about that for a moment. It would take dozens of computers
programmed perfectly and operating together flawlessly to
even get close to performing this task.

Yes, eyes are pretty complicated - that is one reason they are fun to study and understand from a scientific perspective.

The eye is an example of what is referred to as “irreducible
complexity.”

There is no evidence that eyes or any other biological structure are 'irreducibly complex'. Here is a paper describing processes that have led to the evolutionary origins of "phototransduction", the cascade of protein signaling events that results in animals' ability to detect light.

It would be absolutely impossible for random
processes,

It would indeed be difficult for purely random processes to evolve complex systems, but natural selection is not a random process.

...operating through gradual mechanisms of genetic
mutation and natural selection, to be able to create forty
separate subsystems when they provide no advantage to the
whole until the very last state of development.

This is factually wrong. For example, one of these eye "subsystems" provides an advantage to Hydra even though the animal does not possess other of the "subsystems". As mentioned above, Hydra utilizes phototransduction without lens, retina, brain, or even pigment cells. One response to light is for the animal to scrunch into a ball, hypothesized to purge its one-way gut at first morning light. [If there is a designer, at least She had a sense of humor when She made one-way guts - what a great design that is!]. So as evidenced by mouse trap tie clips in the Dover trial; claims of irreducible complexity usually represent a lack of imagination about what sub-systems can do.

Ask yourself
how the lens, the retina, the optic nerve, and all the other parts
in vertebrates that play a role in seeing not only appeared
from nothing, but evolved into interrelated and working parts.

This sounds like an argument against divine design, which claims that eye parts came from dust. In fact evolutionary biology teaches us that proteins of the lens came from other proteins.

Evolutionist Robert Jastrow acknowledges that highly trained
scientists could not have improved upon “blind chance”:

To paraphrase Orgel - evolution is cleverer than you are; that doesn't mean that goddidit. Again, natural selection is not "blind chance".

The eye appears to have been designed; no designer
of telescopes could have done better. How could
this marvelous instrument have evolved by chance,
through a succession of random events? Many people
in Darwin’s day agreed with theologian William
Pauley, who commented, “There cannot be a design
without a designer.”

William Paley, not Pauley. Yes it is truely amazing that evolution produced eyes, and other complex things like livers or brains. Nevertheless, it is a well established scientific fact that evolution did produce these traits.

And this marvelous design occurs not just in humans, but
in all the different creatures: horses, ants, dogs, whales, lions,
flies, ducks, fish, etc. Think about what the theory of evolution
claims: the eyes, in working pairs, of all these creatures slowly
developed over millions of years. Each of them was blind until
all the parts miraculously came together and interrelated with
the others, because all parts are needed for the eye to function.
Then each creature had its two eyes work in harmony with
the brain to interpret those images. Fortunately, each of these
creatures simultaneously evolved whatever matching parts
each would need: sockets, skin, eyelids, eyelashes, tear ducts,
muscles to blink, etc.

Again, Comfort is arguing more against his own claims that against evolution. Eyes appearing separately in every tetrapod is VERY unlikely, but this is what the creationist fable of eye origins would entail. In fact, evolutionary biology teaches us that all living things share a common ancestry, and that shared features usually evolved once, prior to the common ancestor of creatures sharing a trait. This is backed up by mounds of genetic evidence showing shared use of many genes in most animal eyes, including opsin, Pax-6, and many more.

You’ve probably been led to believe that the first simple
creatures had rudimentary eyes, and that as creatures slowly
evolved their eyes evolved along with them. However, that’s
not what scientists have found. Not only is there no evidence


Robert Jastrow, “Evolution: Selection for perfection,” Science
Digest, December 1981, p. 86.

It is simply false that scientists have found the first simple creatures to have had complex eyes. "The first simple creatures" Comfort seems to be referring to are trilobites. There are highly complex arthropods, far far far removed from the first simple creatures. Trilobites are not even the first animals, not even the first arthropods.

of this occurring, but some of the most complex eyes have
been discovered in the “simplest” creatures.
Riccardo Levi-Setti, professor emeritus of Physics at the
University of Chicago, writes of the trilobite’s eye:

"This optical doublet is a device so typically
associated with human invention that its discovery in
trilobites comes as something of a shock. The realization
that trilobites developed and used such devices half a
billion years ago makes the shock even greater. And a
final discovery—that the refracting interface between
the two lens elements in a trilobite’s eye was designed
in accordance with optical constructions worked out
by Descartes and Huygens in the mid-seventeenth
century—borders on sheer science fiction...The design
of the trilobite’s eye lens could well qualify for a patent
disclosure. "

--Riccardo Levi-Setti, Trilobites (Chicago: University of Chicago
Press, 1993), pp. 57–58.

How could the amazing, seeing eye have come about
purely by blind chance? Based on the evidence, wouldn’t a
reasonable person conclude that the eye is astonishingly
complex and could not have evolved gradually, and that each
creature’s eyes are uniquely designed?

Even Charles Darwin admitted the incredible complexity
of the eye in The Origin of Species:

To suppose that the eye, with all its inimitable
contrivances for adjusting the focus to different
distances, for admitting different amounts of light,
and for the correction of spherical and chromatic

aberration, could have formed by natural selection,
seems, I freely confess, absurd in the highest degree."

Even more incredible, though, is that Darwin went on
to say that he believed the eye could nonetheless have been
formed by natural selection. He was right on one point. If a
Designer is left out of the equation, such a thought is absurd
in the highest degree.

Yes, it is still amazing - and still true - that eyes evolved. No natural selection still cannot be equated with blind chance.

At least he included the end of this famous quote, where Darwin writes that anyone with any bit of logical reasoning ability can see that evolution can produce even complicated things.


I didn't spend a lot of time on this because these arguments of Comfort are not worth a lot of my time. They are tired, recycled, un-creative jabs at evolution that have been known to be false for hundreds of years.

In the end, I'll use Comfort's own words to describe what he is doing to evolution. He was writing about Buddhism, but his words apply nicely to his ignorance of evolutionary biology:

Amazingly, the religion of Buddhism [substitute 'Ray Comfort' for 'Buddhism'] denies that God [substitute 'Evolution' for 'God'] even exists. It teaches that life and death are sort of an illusion. That’s like standing at the door of the plane and saying, “I’m not really here, and there’s no such thing as the law of gravity, and no ground that I’m going to hit.” That may temporarily help you deal with your fears, but it doesn’t square with reality.

A few word changes lead to:

Amazingly, the religion of Cameron and Comfort denies that evolution even exists. It teaches that two hundred years of hard work by countless scientists across the globe to elucidate the details of evolution are sort of an illusion. That’s like standing at the door of the plane and saying, “I’m not really here, and there’s no such thing as the law of gravity, and no ground that I’m going to hit.” That may temporarily help Comfort and Cameron deal with their fears, but it doesn’t square with reality.

Cameron Comfort Co-Opt Darwin's Origin

I've had my head in the sand writing revisions of papers before the quarter starts, so I'm sure there is information all over the net about this that I am not integrating here, sorry. But apparently, Kirk Cameron and Ray Comfort have co-opted Darwin's ..Origin of Species... and inserted creationist propaganda into in introduction that is mixed with some facts (i.e. biographical facts on Darwin). It also includes propaganda linking Nazi-ism and evolution, etc.

They plan to had out published copies at the 'Top 50' research institutions in the US. Cameron in a video mentions he will come to a local university personally (here at UCSB? UCLA? I'm not sure what "local" is to Mr. Cameron).

Apparently, Richard Dawkins has been involved in getting the word out to evolutionists to expect this, kudos to him and his crew for doing that.

I personally disagree with the plan of action I'm told Dawkins' camp is promoting (I haven't confirmed that he is actually promoting this). That plan entails obtaining as many copies of the book as possible and removing the Comfort introductory propaganda.

In my opinion, this is not a good strategy. It seems that this could look desperate, as if scientists actually have something to worry about (when it comes to the facts of evolution, we do not have to worry), and it looks like book burning or censoring.

Instead, I think a concise pamphlet refuting the bogus claims of the introdution would be outstanding. It could have references and web links, and could also expose what I see as the breathtaking inanity of Comfort and Cameron's crusade against critical, rational thinking.

It would be great if someone like the NCSE were involved. Time is short and an organized response would nice.


Below, I attach an email that was sent around here at UCSB, which includes web links to some of this stuff:


Colleagues,

We all loved Kirk Cameron on Growing Pains:
http://www.youtube.com/watch?v=6Vo2i3NFq78&feature=related


Years later we were amused and perhaps a bit alarmed at his
'Origin of the Banana' video:
http://www.youtube.com/watch?v=2z-OLG0KyR4
(That's Ray Comfort there with him)

But in November of 2009 he and Ray Comfort are taking it to the
next level: http://www.youtube.com/watch?v=GN9zpf5cT0M

The Important thing for us: *THIS GIVE AWAY WILL HAPPEN AT
UCSB! On November 19th!
*
Richard Dawkins has proposed a strategy: Collect as many of these
books as possible, remove the 50 page intro and donate the copies
to schools, libraries, or the whoever
(http://www.facebook.com/group.php?gid=155609217391)

We can stick with this strategy or come up with something else but
we should do *SOMETHING*

Basically we need to get organized if they are coming here. Ready
with information &/or to get these books. Ready with pamphlets
answering his questions or just trying to keep them off campus?

*Who would be into meeting within the next couple of weeks to
start to get ourselves organized?*

If you are not ready for action now here are some highlights from
Comfort's 50 page Intro:

1) So, even though we share 96 percent of our genetic make-up with
chimps, that does not mean we are 96 percent chimp. Be careful you
don’t fall for the illogic of this “evolutionary proof,”
2) here are some interesting questions for the thinking
evolutionist: Can you explain which came first—the blood or the heart—and why?
3) You’ve probably been led to believe that the first simple
creatures had rudimentary eyes, and that as creatures slowly
evolved their eyes evolved along with them. however, that’s not
what scientists have found.

Phylogenetics Conference - Seattle

Actually, the meeting is more general than "phylogenetics", but I'd like more phylogeneticsts to attend (and this was my "campaign" platform when running for secretary of the division of systematic biology. "Campaign" is quoted since I'm less than 100% positive I wanted to win). The title of this blog post is an attempt to get people from dechronization interested in the conference- this blog is on their roll, so the title appears.

The meeting is the Society of Integrative and Comparative Biology (formerly American Zoologist), which will run from Jan 3-7, 2010 in Seattle.

Note the abstract deadline of Sept 11 2009. This is often a hard deadline without extensions!! So we'd better get crackin'!


Strengths of the meeting are student funding and in general its being student friendly. Topical strengths include physiology (comparative), evo-devo, and invertebrate biology. Given my interest in eye evolution in inverts, it's become my main meeting. There is often a strong showing of phylogeneticists, usually those using phylogenetic tools to address comparative biological questions, with fewer people presenting on phylogenetic methods for methods' sake, the strength of the summer evolution meetings.