Friday, March 20, 2015

Little League Ethics


Our local Little League does not have lights to play night games. Because baseball cannot be played in the dark, the lack of stadium lights imposes a highly unnatural rule on some of our baseball games: a time limit.

One of the truly beautiful things about baseball (besides that the defense has the ball!) is there is not normally natural time limit. It's what led Yogi Berra to say “It ain't over til it's over”. In typical Yogi style, his famous quote makes no sense and perfect sense, all at the same time. A team always has a chance in baseball, even when down by a huge margin, if they can just score enough before their final out.

It truly ain't over til it's over.

Until there is a time limit.

A time limit in baseball changes everything. It raises strategic and ethical dilemmas: Is it ethical to stall to try to reach the time limit and preserve a win? Is it ethical to purposely speed up the game to reach the time limit and preserve a win?

I have encountered these ethical questions forced by Little League time limits, and these ethical questions to me are critical. In my life, I strive for excellence. One goal is to achieve excellence in sportsmanship and ethics – especially in Little League. By definition, excellence is not easy to achieve. Excellence requires dedication. Excellence requires plain old fashioned hard work. Excellence requires a lot of thought and discipline. Excellence is the highest achievement for which I can strive, and I can think of fewer more important goals than setting an example of excellence in sportsmanship and ethics for our youth. This is serious.

In a baseball game with a time limit, the visiting team can take the lead in the final inning – only to have the game revert back to penultimate inning – resulting in a loss – if the time limit is reached. This is highly unnatural in baseball, but it does come up. Many tournaments must be on a time limit. Rain storms sometimes even impose time limits in Major League Baseball.

After much thought, I believe that speeding up a game intentionally under the rules, even in Little League, is ethical. I believe that slowing down the game intentionally is less clearly ethical, but can mainly be moderated by the umpire anyway.

Here is an example. My team will be the visiting Brewers, the home team will be the Giants. Going into the last inning, the home Giants are winning 8-6. The sun is going down, and the rule is that when the ambient light gets low enough, an automatic light goes on. When that light is on, there is one more batter. If the game's final inning is not complete, the score reverts back to the last complete inning.

On this night, the Brewers stage a valiant comeback. There was a walk or two, but our Brewers were hitting and running and scoring. They were jubilant. They had taken back the lead in dramatic fashion. Yogi was right, it wasn't over! Life lesson speeches on not giving up write themselves after comebacks like this one. This kind of come back is beautiful. It is powerful.

The Brewers went up 11-8, with only 1 out in the last inning! But now the ethical dilemmas start. If time runs out, the Brewers lose. Once that light goes on and the umpire calls the game, the score reverts back to last final inning. The comeback – officially – is erased. But it is not erased from the minds of the Brewers. It is not erased from the minds of the Giants. The rule is for safety, so there are no games after dark, and so umpires don't push it. But tell that to Alex when his game winning hit is nullified. Tell that to Andre, when his game-tying run no longer counts. Let the games begin!

It's the final inning. The Giants' coach takes a leisurely stroll to the mound to talk to his pitcher. And most of the defense. While infuriating to the opponents, a coaches' visit is well within the rules. It might even be advisable to calm down the pitcher and the defense. I conclude such a visit is ethical. However, the umpire MUST keep a tight leash on how long such a visit can last. Stalling must be controlled by the umpire, but I do think it is actually ethical for the team with that advantage to slow down a little bit: within the rules and within reason. What if a coach tells a kid to tie his shoe 4 times? This is pushing the limits dramatically now. But here again, I believe the umpire can have some control on the stalling. He can yell “play ball”. If the kid is tying his shoe on the base, that is his team's disadvantage. If a batter will not get in the batters box, the umpire can allow a pitch, and call a strike for each one. Soon, pitch timers will be part of the major leagues, like shot clocks in basketball. So, I don't believe there is strong ability for a team to stall the game with a strong umpire who keeps a lid on it. Of course, a stalling team could purposely try very hard to get no outs and prolong an inning indefinitely. Although the other team could counter, I think this would now cross the line for me into unethical. The stalling team would be purposely failing in order to salvage a win on a technicality: a time limit.

Now, what about the team that went ahead with a fight to the end and a dramatic come back, our visiting Brewers? Can those Brewers ethically speed up the game to bring the end more quickly? I believe this is ethical. After taking the lead by three, can they purposely make their final two offensive outs to get on to the field faster, and try to get their final three defensive outs in time? Can they purposely steal a base when they think there is a VERY strong chance they will be thrown out? Can they purposely strike out, no matter where the pitch is thrown? Or is asking kids to do that for the team going too far?

My instinct tells me rushing to outs is, in fact, an ethical tactic. Unlike excessive stalling, it is striving to finish the game to AVOID the technicality. It's striving to finish the game naturally, before getting to the time limit. In the words of the Little League pledge, it is “Striving to Win” – and I believe it is also “Playing Fair”.

I read an interesting story on Little League ethics that parallels my thoughts. I won't recount the whole story, but the link is here

http://www.ethicsscoreboard.com/list/littleleague2.html

Without retelling the entire story, one quote is particularly apropos, edited slightly to fit this current situation
“True, [running into an out or striking out purposely] was superficially a violation of the League's "strive to win" ethic, but in this odd instance it was really the opposite: only by [quickly making outs] could his team win.”

Of course trying to win cannot dictate everything. It has to be within the rules. But clearly, trying to steal a base is within the rules, and striking out is also.

The link to the ethics story also points out an interesting parallel. When we ask a player to perform a sacrifice bunt, s/he is purposely (probably) making an out for the betterment of the team. I maintain that getting outs quickly to finish a game before a time limit is in fact directly akin to a sacrifice bunt. I'd like to award Jack a sacrifice steal, and Justin a sacrifice strike out.

This is important to me. I want to do the right thing. I believe sacrificing for the good of the team is noble. I believe striving to win is critical to sport. I believe fighting to avoid the nullification of a brave and jubilant comeback is itself noble and ethical. I believe in running into an out. I believe in a quick strike out. I believe in the sacrifice bunt.


And I would fight that fight again.

Friday, November 7, 2014

Question on Independent Origins Test

We just published a paper on convergent evolution, which uses a new test of convergence called the "Independent Origins Test". In the main text, the description of the test is limited (however see the supplement).

Just now, I received a question about this test, and I paste my answer below, in case others might benefit from the answer.

THE QUESTION: Dear Dr Oakley I read you article:  Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid (great!)


I do not undestand the logic behind this
The observed data are approximately and conservatively 5,000 times less likely to have arisen from an evolutionary history with less than three gains of photophores than from an evolutionary history with three or more photophore gains 
we should compared 1 gain (ancestral) follow by 8 losses versus 2 independent gains here you compare less than 3 gain (1 or 2 (which is the case here)
versus 4 ,5 ,6 
could please tell me what am I missing


THE ANSWER
  Yes, the traditionally more common way to frame alternative hypotheses to test independent origins is to compare the likelihood of X gains versus Y losses. This is what we did for example in Oakley and Cunningham (2002) 

    However, the "independent origins" test in this 2014 paper frames the alternative hypotheses in a different way. The alternatives are: 1 gain of the trait (= homology) versus more than one gain (=independent origins). The test calculates probabilities (assuming the model of trait evolution, the phylogeny, and the distribution of traits on the tree) of these alternative hypotheses.

    Why, you might ask then, did we compare the probabilities of "1 or 2 gains" to "3 or more gains"? The general reason is to be conservative.  More specifically, in the case of these squid, there is a clade where photophore might have evolved more than once within that clade itself. This was not the focus of the paper, and we were really interested in whether two distantly related clades (loliginids and sepiolids) evolved photophores separately. Since the independent origins test counts total number of gains on the entire tree, it was not distinguishing between two gains in those distant clades versus a separate gain within sepiolids. To be conservative then, we reported the probability of at least 3 gains. Examining "at least 2 gains" would yield even higher differences between alternative models.

    I believe the easiest critique of this approach is the simplicity of the model, which assumes the same rate of character gain and loss for the entire tree. In simulations I have done (a la Simmap), a little bit of homoplasy on a tree leads to estimated rates of trait evolution that require HUGE numbers of gains and losses on a tree, to the point of being biologically very unrealistic. I believe that models that allow different rates of evolution on different parts of the tree could do better at yielding biologically realistic rates of trait evolution. See for example Skinner (2010) 

Friday, December 27, 2013

Starting a lingustic foray into evolution - cray cray?

This holiday season, I've learned a new word from my nephews, and that word is 'cray-cray'*. According to my nephews, and the Urban Dictionary, cray-cray means 'really crazy'.

Researching this word has led me - yet again - to some parallels between evolution and linguistics. I want to start documenting these parallels more formally, because I think it could be important. My biology research is focused on how new traits originate during evolution, sometimes called 'evolutionary novelty'. How did eyes originate in evolution? How about hair or milk? Although I could be cray-cray, I believe this area of evolution has received less attention than other areas, and the theory and concepts are underdeveloped. Yet in linguistics, it seems novelty is a central area of theory.

Cray-cray is a new word, a novelty. Languages change so fast, with such full documentation, it seems as though linguists have a richer theory for explaining how novelties arise. One aspect of novelty in linguistics is called Word Formation, and there are several ways in which word formation occurs. I believe many of these have parallels in organic evolution, although they may not generally be differentiated or articulated. I want to explore that on future posts.

Craycray seems to be due to a particular type of word formation that is not particularly common in English, called reduplication. Actually, as I read and understand further, it seems reduplication is considered to be a change in grammar, and not as a mechanism of word formation. From this perspective, cray cray is not a new word, but is rather a grammatical change to convey a new meaning. In both evolution and linguistics, it seems challenging to think clearly and consistently about structure (word) and function (meaning) and their relationship to each other.

Reduplication is quite common in many languages, and is used in several different ways. Our cray cray example seems to be reduplication for the purpose of intensifying a noun. I don't think this is common in English. Wikipedia gives an example from Hebrew, where Gever means 'man' and 'Gever Gever' seems to mean something like a man's man or a manly man, or perhaps a macho man. A man, intensified, just as cray cray means crazy, intensified.

According to the same Wikipedia site on reduplication, there are some English examples of reduplication. We mimic baby talk, as in 'bye-bye'; use rhyming reduplication, as in super-duper; or sometimes change the vowel sounds in the reduplication, like zig-zag. An interesting example is the 'schm' reduplication - adding 'schm' to belittle something, or to indicate irony: 'craycray, schmacray - I can just say lunatic'. Schm-reduplication is said to be 'productive', because it can be used with most any word. We also use reduplication to clarify a literal meaning versus a figurative meaning. An example that comes to mind is to clarify hot - 'do you mean spicy-hot or HOT-hot'?  HOT-hot is clarifying the meaning as temperature. By the way, I think we should adopt the Spanish word picante to mean spicy-hot, a word we need in English!

Besides cray cray, I can't think of any other examples in English of intensifying reduplication. From that perspective, it might not actually be reduplication, since reduplication refers to grammar. In English, our grammar doesn't usually intensify using reduplication, so cray cray perhaps really does fit more into Word Formation. But I also cannot fit it into established modes of Word Formation, either, such as those explained on Wikipedia or a Rice site (by the way the Rice site counted zig-zag as compound word formation, not as reduplication). Instead, cray cray is part clipping - taking just part of a longer word, like ad for advertisement, or dis for disrespect - and part compounding - putting two words together, like phone booth. Crazy clipped is cray and compounded is cray cray.

My purpose here is to understand novelty in linguistics to draw parallels to evolution. For example, thinking genetically, I know that protein domains are often 'reduplicated' within the same gene. It will be interesting to think this through and research it. What types of function can protein domain reduplication provide? Are the biological-functional implications similar to linguistic-grammatical implications? I believe intensification of biological function does happen by domain reduplication (I can think of some examples, that I won't go into). But what about other parallels? That will perhaps be the subject of a future post.

I should end now before this post is so long as to be cray cray.






* I believe this is mainly a spoken word, such that the spelling is not yet standard. It could be craycray, cray-cray, or cray cray. 

Thursday, December 26, 2013

The resurrection of Evolutionary Novelties

I've decided to resurrect the Evolutionary Novelties blog. While I wrote fairly regularly from late 2007 until 2009, I stopped writing any blog posts after that. Although I didn't specifically plan the regular writing sessions or the hiatus, I've felt lately that I would like again to use this forum to share some ideas.

Why the hiatus? Blogging changed my brain

Late in 2009, I began to feel that blogging changed my brain in ways that I did not like at the time. Namely I felt like I was thinking too much about blog posts. Blog posts - at least good ones - are short, punchy and catchy - like a quick sprint. Yet conducting research and writing scientific papers takes dedication and persistence - like a marathon. When writing Evolutionary Novelties posts regularly, I began thinking about posts a lot; so much I felt like it was taking 'thinking time' and writing time away from my research. Professional research takes a huge amount of thinking time, from brainstorming to problem solving to deciding how to pitch grant proposals and publications.

There are also two more mechanistic reasons I took a hiatus from writing blog posts. First, I got my first smart phone around that time. Instead of doing a lot of reading (email, news, papers, other blogs) on a computer with a keyboard at the ready - I began reading on a mobile device. Without a keyboard under-finger, the possibility of a response became less immediate, and my habits changed. The second mechanistic reason is personal. My son grew to genuinely love playing sports and following professional sports. This rekindled my childhood love of sports, and I've come to spend much more time coaching, playing, and following sports. Following and participating in sports also competes for my online time, and my 'thinking time', so writing blog posts fell away.


Why the resurrection? I have things to say

Writing blog posts can be a great outlet for certain topics, and some such topics have become priorities for me.
  1. I feel I am becoming a good mentor, and I would like to share more broadly mentoring advice. Well, actually, I think I've always been pretty good at mentoring because I genuinely care about the people I mentor, I care about their careers, and I generally have good instincts about career decisions (it's something I think a lot about). I also sometimes worry that with more students and postdocs in my lab, that there is not enough time for me to be effective at mentoring everyone all the time. Pointing to a blog post with career advice might sometimes be effective, and might help people outside my lab. In this regard, I've been inspired by Sociobiology.
  2. I've lately focused my research efforts and ideas more squarely on my 'home group' ostracods, and I'd like to share more about their amazing biology. During the golden era of Evolutionary Novelties, I wrote about these animals in a series I called 'ostra-blogs'. I'd like to continue this part-travellogue, part nature writing series because we've had some fun adventures lately. My students have also expressed interest in writing ostra-blogs, and they make a good vehicle for possibly telling the public about ostracods (or is it ostracodes?).
  3. I want to document ideas about parallels between Evolutionary Novelties and the linguistic novelties. I have a long-term goal to write a book that teaches concepts of how new things evolve, using examples from linguistics. I need to learn and remember a lot about linguistics before that can happen.
So, I am going to try to find the time to contribute to Evolutionary Novelties more regularly. At least until I want my brain back again for other things...

Thursday, November 21, 2013

Unfortunate arbitrariness at NSF costs our graduate students

Last week, a student in our lab had an NSF DDIG (Doctoral Dissertation Improvement Grant) returned without review. The reason is the proposal did not fit the goals of the panel, according to the program officer. Unfortunately, the PO thought the proposal fit more squarely in a different panel, which does not accept DDIG proposals. To me, this points to a very unfortunate difficulty at NSF, which is that in the IOS (Integrative Organismal Systems) division, only one panel - Animal Behavior - accepts DDIG proposals. This puts the Animal Behavior Program Officers in a difficult position: They are forced to define discrete boundaries to a scientific field. While all fields are a continuum, defining discrete fields within the division of "Integrative" biology seems particularly arbitrary because the very definition of the division is to use multidisciplinary perspectives.

This week, I learned through social media that the students of multiple colleagues experienced the same rejection without review. I know how hard students work on these proposals, and to have them returned without review is a disservice to the students who are the future of our disciplines. On one hand, it reinforces a mantra that NSF promotes - "always contact your program officer". Yes, I certainly should have checked that we were within the scope of the panel. That said, my excuse is that I really didn't imagine, as I will describe briefly below, that our proposal on the evolutionary and genetic basis of behavior would not be considered animal behavior. But this points to the challenge - the current structure forces an arbitrarily discrete definition of a field. According to the call "In the Division of Integrative Organismal Systems (IOS) only proposals within the scientific area of animal behavior supported by the Behavioral Systems Cluster are eligible."

What is (Animal) Behavior?

Since I am a newcomer to behavior (through training in evolution and phylogenetics), I've actually been wondering a lot about the question of what is behavior.  What about bacteria that follow chemical cues? Is that behavior? Do plants or slime molds behave? Viruses? I think they do. The NSF panel has the word "animal" in it, which would rule out these questions (even that seems arbitrary to me). But still there are ambiguities. Do light-following, swimming sponge larvae that lack nervous systems behave? What about annelid worm larvae or box jelly larvae that have ciliated cells that respond to light? In these animals, a single cell acts as a sensor (light) and a motor (cilium) to cause swimming. Is that behavior, or is that physiology? To ask interesting questions about these systems, we don't need to classify it into a field. But to get a DDIG proposal funded, a student is restricted in the questions she can ask.

My student's proposal walks the line between behavior and physiology, a little bit. But the student and I both feel very strongly that we are studying behavior (even animal behavior, since these are cephalopods). Here are the first few lines from the project description:

"Cephalopods dazzle prey, woo mates and seamlessly blend into the background using skin that changes in both color and texture (Hanlon and Messenger, 1998). These diverse behaviors in cephalopods and countless others found throughout animals inspire the question of how new behaviors evolve to produce the riotous variety we see today (Tinbergen, 1963). Do novel behaviors stem from evolved mechanisms? Or do new behaviors primarily arise through evolutionary “tinkering”, which may co-opt, retool and recombine existing mechanisms and modules? Answering these questions is fundamental to understanding how behaviors evolve."

Our goal really is to understand how behaviors evolve, especially at the genetic level. Yet the program officers write:
"... As written, this proposal does not address questions or theory in the field of Animal Behavior. Thus it is not appropriate for this competition and is being returned without review."
and yet, here is how the NSF Behavioral Systems Cluster describes its goals (my emphasis):
The Behavioral Systems Cluster supports research on the development, function, mechanisms, and evolutionary history of behavior, with emphasis on a vertically integrated understanding of the behavioral phenotype in nature. To foster this integrative goal, the Cluster specifically encourages projects that seek to understand how combinations of neural, hormonal, physiological, and developmental mechanisms act synergistically as a system from which behavior emerges.  Laboratory work or the study of animals in captivity is encouraged, to the extent that it contributes to the understanding of behavior in natural systems.
I still feel our proposal addresses questions in the field of Animal Behavior. Yet, I recognize the root of the problem is that only one area in IOS accepts DDIG proposals. This forces a line to be drawn somewhere, and even if our proposal is animal behavior, there must be discrete decisions about where animal behavior ends that will affect someone.

A broader view

National Academy Member, David Hillis of the University of Texas, astutely pointed out that the current difficulty points to a fundamental decision about funding many small grants or funding fewer larger grants:

"The problem, as I understand it, is that only DEB and part of IOS make the case that DDIGs are worthwhile. To me, they are perhaps the best use of NSF funds, and result in the highest return for the buck of any federal funding. But the science communities (outside of DEB) need to make this case to NSF, if they agree. There is much more of a tradition of independent research by graduate students in the fields represented by DEB, compared to many other areas. I've heard that some other programs resist DDIGs because they disperse a small amount of money per proposal, so they have a relatively high administrative cost per dollar of research funds dispersed, and graduate students are much less likely to be doing truly independent research outside of DEB. But I think any increase in admin costs is more than made up by the high return in each dollar used, which I think is far more efficient for DDIGs than most other programs. The trend at NSF is actually in the opposite direction: funding of very large, multi-institutional grants and centers. I think these probably result in the least efficient use of research dollars (certainly far less efficient than DDIGs, in my experience). But that balance may differ among fields, which is why DEB makes the argument for DDIGs, but most other programs don't. "

I wholeheartedly agree with those comments. Supporting DDIG proposals is a very wise investment, not only to fund up-and-coming researchers, but to provide a platform to learn how to write grants, to learn about the NSF funding system, and to promote early independence in scientists. As such, I very much advocate expanding the DDIG call to all of IOS.

Action

So, what can I/we do besides complain about the situation on an obscure blog? I propose to organize anonymous peer reviews for those students whose DDIG proposals were returned without review. For the students in this situation to whom I've spoken, this is their biggest regret: They worked hard and cannot even get feedback. I propose to facilitate obtaining that feedback. Hey, maybe we could get really creative and start a Kickstarter (or similar) program to *actually fund* some or all of the top reviewed proposal. Here is what I propose:

  1. Any student whose DDIG proposal was rejected without review can send their proposal to me by email on or before December 2. I imagine they can just download a pdf from fastlane and send it along to me. I will treat the proposal as confidential, just as I would if I reviewed it.
  2. I will act as a sort of 'program officer' and solicit 2 or 3 anonymous reviews per proposal. I will ask reviewers to follow precisely NSF reviewer guidelines and make sure they keep the grants confidential, just as if NSF asked them to review. The reviewers will be anonymous to the student.
  3. I will summarize the reviews and send them back to the student. The goal is for them to get feedback about their research ideas from anonymous reviewers.

In addition to providing the students with feedback, and an idea of how their proposal might have reviewed, another goal is to raise awareness of what I see to be unfortunate arbitrariness that is costing our graduate students.

If you are willing to help, here is what you can do:
  1. Volunteer to serve as an anonymous reviewer of proposals. Just send me an email: oakley@lifesci.ucsb.edu and tell me you are willing
  2. Spread the word, so that affected students can hear about this and get their proposals reviewed, if they like.
  3. Contact NSF and tell them you support expanding DDIG to all of IOS.
  4. Send any additional ideas or concerns to me by email or as comments on this blog post

Thank you for listening!
Todd Oakley, Professor, UCSB

Wednesday, December 23, 2009

Ostra-blog 9. Postasterope barnesi

It's unfortunately been too long since I've posted an 'ostra-blog', a post about my main study group, the Ostracoda. If you haven't seen these, I encourage you to read some of them. Most contain little anecdotes, personal vignettes about interesting experiences I've had with ostracods.

Try this link, if you interested.

This installment is a quick post inspired by a colleague who is trying to collect bioluminescent Vargula (subject of previous posts). He did some plankton tows out by Catalina Island, and came up with some ostracods, but these are a different family. See our exchange below, and a picture sent by his student:


The query:
Hi Todd,

I apologize for the out of focus, low magnification photo attached -- but is it likely that these ostracods are Vargula tsuji? These are not from a trap, but instead from night surface plankton tows from the dock at Wrigley. These are quite large for ostracods (up to 1.5 mm or so in length, I'd guess), fairly bright orange, and very abundant in the plankton soon after dusk.

Thanks for any simple confirmation/rejection of our tentative id. I appreciate it. Sorry again for the low quality image; I'm not at Catalina or I'd take a better one. This was sent to me by a student.



The Picture:



The reply:

No, those are not Vargula, which is in the family cypridindiae. These that you found are in the family cylindroleberididae. I think the common sp out at Catalina is Postasterope barnesi, and this looks like it could be that species. Both are myodocopids, which are larger than the somewhat more common podocopids...

I've found males of this family to be attracted to lights at night. Most myodocopids mate in the water column after sunset, and the males of some sp are attracted to lights. Probably just about all the individuals they found are males, I'd guess. The one pictured looks like a male, based on the tapered carapace (hard for someone to see who hasn't looked at a million ostracods). But an easy way to tell a male in these is that the males have a REALLY long sensory bristle. It's a "hair" (2 actually, one on each side) that emerges from the front of the carapace along with the swimming appendages. But this sensory "hair" is really long, longer than the body in many cases. I actually can't tell from this picture if there are the long sensory bristles because of the focus, but I'll bet they are there... I do see a white line across the carapace in the right spot, but I can't tell if that is part of the swimming appendage, or the sensory bristle....

Friday, November 27, 2009

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.