Sunday, June 12, 2005

Reverend William Paley's Circadian Clock

I got homework to do. PZ Myers alerted me to an incredible argument that the existence of circadian rhythms denies evolution!

bryanm, the proprietor of the aptly-named The Narrow blog, describes himself as "...nobody who wants to tell everybody that there is somebody who can save anybody." In other words he is a know-nothing who keeps bothering everybody trying to push his idea that there is this non-existent being who can save anyone from whatever one wants to be saved from except from the nagging by bryanm. The other day, he wrote this post densely packed with nonsense. No need to look around the blog - it contains mostly stuff debunked here and here.

This is what bryanm writes in one of the comments to his post linked above:
Finally, let's look at circadian rhythms and the age of the earth. Investigation of nearly all of the earth's living organisms including microorganisms, plants, animals and humans) reveal the existence of circadian rhythms or biological clocks Numerous scientific studies have clearly deomnstrated that these circadian rhythms are not only widely present in all life forms, but are resistant to any and all external changes in the environment. Studies have shown that these biological rhythms are also endogenous or built-in genetically. How did these 24 hour rhythms get there in the first place? Obviously, they had to have been programmed initially into all biological life forms by the Creator (Jesus Christ) himself.

Arrrrggh! Where do I start? Let me dissect it first point by point, and finish with a Big Piture in the end.
Finally, let's look at circadian rhythms and the age of the earth.

Thankfully, PZ already debunked the "leap second" argument, so I don't have to deal with it here, but read the counter-argument here for your own edification. Although the length of the day did change somewhat over billions of years, the change is so slow, the day was NEVER shorter than about 18 hours. The rate of change is so slow that it is easy to evolve the changes if you needed to. But, you don't need to! Guess what? Even a well-buffered circadian system in a complex organism CAN entrain to 18 hour cycles! I did it in Japanese quail (Zivkovic et al. 1999). The confusion is between freerunning period and ability to entrain to environmental cycles. The day is 24 hours long. Endogenous circadian rhythms range between 16 and 32 hours in period, yet each one easily entrains to the 24-hour light-dark cycle. The endogenous period does not need to be equal to the length of the environmental cycle. Actually, a circadian clock with exactly 24 hours period will be VERY difficult, if not impossible to entrain. The mechanism of entrainment relies on daily correction of error - the difference between the endogenous and exogenous cycle is reset every day. For more, read the Entrainment posts here.
Investigation of nearly all of the earth's living organisms including microorganisms, plants, animals and humans reveal the existence of circadian rhythms or biological clocks.

First, circadian rhythms are ubiquitous in only four out of six big Kingdoms of Life (Animals, Plants, Fungi, Protists) and only a small group (cyanobacteria) from a fifth Kingdom (Bacteria) has evolved a circadian clock:
Archaea and most Eubacteria are arrhythmic. For Archaea, the explanation might lie in their ecology - they usually inhabit the most inhospitable regions of the planet including deep-oceanic hydrothermal vents, deep soil, rocks, salt deposits, polar regions, underground hot-water springs, where the rhythms of the planetary surface might not have any direct effect on their survival. Some Cyanobacteria have circadian rhythms as they need to temporaly separate incompatible reactions of photosynthesis and nitrogen fixation (Johnson and Golden 1999). Real Bacteria, being Prokaryotes, might just be capable of a rapid response to the direct environmental fluxes, and a timer might impose too rigid a control in, on their scale, essentially unpredictable environments.

In other words, circadian rhythms are adaptations of complex organisms to life on the surface. If you are too simple, or if you do not live on the surface, you do not need the clock. Circadian rhythms gradually decay in subterranean and cave animals (just like cave fish loose eyes).

The genes involved in circadian rhythms in the five Kingdoms are completely different, suggesting that the biological clock evolved independently five times in the history of life on Earth. The internal logic of the clock, though, is somewhat similar, usually involving some version of a transcription-translation feedback loop between clock genes that generates rhythms in the cell (and organism) which, in turn, feeds back onto the genetic feedback loop.

Looking at a complex circadian system, e.g., that of mammal, reveals not just great complexity, but also great redundancy: multiple copies of the same clock genes, one copy of which can always be "knocked-out" with no apparent effect on the workings of the clock. If you knock out all redundant copies out of a mammalian clock you will still have a functional, albeit much simpler, circadian clock that is VERY similar to that of a fruitfly.

It is much more revealing to look at the simplest clock, that of cyanobacteria. Cyanobacteria have a unique problem to solve: their life depends on succesful activity of two different biochemical processes - photosynthesis and nitrogen fixation. Unfortunately for them, these two processes are incompatible with each other, thus need to be separated. Most cyanobacteria have solved the problem by forming chains of bacterial cells. A division of labor evolves, in which each cell is able to remain relatively simple and specialized for one of the two processes. Some cells do only photosynthesis, others only nitrogen fixation. The two types of cells then exchange the final products (energy and nutrients).

However, a small number of cyanobacterial species (e.g., Synechococcus and Nostoc) have hit on a different solution. They do not form chains. Each cell performs both functions (and is thus more complex). Instead of spatial separation, they evolved temporal separation of the two processes: photosynthesis happens during the day (when sunlight is abundant) and nitrogen fixation is relegated to the night period. From what I remember from bacterial literature, about 2/3 of the genome is expressed ONLY during the day and about 1/3 of the genome is expressed ONLY during the night. This clock is, thus, just a simple ON/OFF switch: switches light-compatible genes on and nitrogen-fixation genes off in the morning, and the reverse in the evening. That does not sound irreducibly complex any more, does it?

Numerous scientific studies have clearly deomnstrated that these circadian rhythms are not only widely present in all life forms, but are resistant to any and all external changes in the environment.

The blades of knives, spears and swords had to be made very sharp, because our skins are resistant to hits by blunt objects. My body temperature is alaway around 37 degrees Celsius, no matter what the temperature is outside. My blood levels of Calcium are practically constant and taking TUMS does not change that. My blood pH is fantastically resistant to change, although I drink liters of highly-acidic Coke every day. Some people's brains are highly resistant to change by presentation of facts that challenge one's prior beliefs. Yet, all those systems have evolved. How does resistance to changes in the environment have anything to do with their evolvability? If brianm took a pill of Lithium, his endogenous freerunning circadian rhythm would dramatically change. Yet, that is not important - what is important is that brainm's circaidan rhythm, with or without Lithium, is highly malleable to environmental change: its "natural" period of about 25 hours is "forced" by a light-dark cycle to assume a 24-hour period EVERY DAY. Entrainment is the most obvious example of malleability of the circadian rhythms.

Also, brianm is confusing resistance at the time scale of an organism's lifespan and resistance at the time scale of evolutionary change. Even if endogenous rhythms were highly rigid within an individual, that has nothing to say about the ability of natural selection to alter its properties over many generations over a large period of time.

But they are not rigid even at the time scale of individuals. Most of my PhD dissertation (nothing published so no details here yet, sorry) is based on the study of individuals who exhibit marked day-to-day variability in period. Those individuals have been discarded by past researchers. I can now walk into the room with hundreds of quail and pick, with over 80% success rate, just by looking at them, which ones have stable rhythms and which ones have variable rhythms. I have even higher success rate in predicting who is who BEFORE they hatch out of their eggs! I can breed them for or against this trait - what more can one ask?

Studies have shown that these biological rhythms are also endogenous or built-in genetically.
which eliminates external factors, be it "Factor X" or Aliens or Designer-God. We know the genes and we have tracked how they evolved. Something being "genetic" makes it easier to explain by population genetics than traits not directly attributable to individual genes (e.g., emergent properties of a complex system).
How did these 24 hour rhythms get there in the first place?

I have written about it before:
There are three main lines of thought concerning the origin, evolution and adaptive function of biological clocks (Winfree 1990). The first view assumes that in the beginning the organisms were arrhythmic. The cyclic nature of energetic availability and cycles of potentially degrading effects of the sun's ultraviolet rays on particular pigmented enzymes, provided the selective environment. A cell with a timer can predict the changes and adjust its metabolic activities to minimize energetic and material loss. This cell will outcompete the other cells in the Archeozoic sea (Pittendrigh 1967). The emergence of such a system so early in the evolution of life leads to prediction that the molecular mechanisms of circadian rhythmicity will be highly conserved among all organisms (Winfree 1990, p.389).
The second view assumes that the environment itself forces rhythmicity onto the early unicellular organisms (Goodwin 1966). To economize waste, the cell evolves modifier genes. Each of these gene products will have a role in facilitating a smooth transition from one to the next phase of the imposed cycle. As more and more such genes evolve, every state of the cycle comes under genetic control. Three billion years later "the cell might surprise itself to discover...when some scientist first puts it into constant conditions, that it shuffles its way spontaneously through almost the same cycle" (Winfree 1990, p.390). So, even though all the cogs and wheels were, the whole clock itself was never selected for.
The third view states that all biochemical processes are cyclic. Furthermore, this cyclicity is part of the definition of life. Some of the cycles are regular, and the periodicity of such oscillations can be modified by natural selection (Winfree 1990, pp.391-392). Flexibility in counteracting stabilizing homeostatic mechanisms can add another degree of freedom in which to search for optimization. The second and third views expect to see almost as many circadian mechanisms as there are species. If one speculates that the life originated in the shallow tidal pools, than the circatidal rhythms might have been the first to arise, either before or simultaneously with the circadian clocks.
There is nothing incompatible between the three views. They could have conceivably all contributed to the emergence of timing mechanisms.

The problem in chronobiology is that the adaptive function of clocks is so obvious that it is difficult to get funds for rigorous testing of evolutionary hypotheses. The circadian clock is one of the best understood biological mechanims at the molecular level, so evolutionary relationships between the clock genes are too easy to see. Actually, I have lamented before that not enough rigorous evolutionary research is performed. For instance, I wrote this in 2001 as an answer to one of the questions on my written prelims, and posted it here as a blog-post later. Carl Johnson recently published a review with the same sentiment, ably reviewed by Heinrich, not Hindrocket on his blog, again voicing the same sentiment. The problem is not that it is difficult to explain the origin, evolution and adaptive function of clocks. It is the opposite - the embarassment of riches! So much is known. There is so much variation. There is such a good match between one's circadian function and one's ecology. It is the one biological property that I would pick to conveniently forget to mention if I was a Creationist.
Obviously, they had to have been programmed initially into all biological life forms by the Creator (Jesus Christ) himself.

How did Jesus Christ manage to create a world which he was to be born into a couple of thousand years later? I can see the argument that his Daddy did it, but Jeebus himself? Makes no sense. I like the use of the word "programmed" - I can just imagine the Big Hacker In The Sky playing with code on his huge computer that never freezes and gets no viruses ever. Is all of Creation just God's blog?

What brianm got hooked on was the term "biological clock". This is the favourite Creationist example ever since Paley wrote about the Watchmaker. What a coincidence: if there is no watch without a watchmaker, there cannot be a circadian clock without a circadian clockmaker. Hey! Just because we use metaphors and call a cell-component a machine that does not mean it actually IS a machine. It's a metaphor!

And, actually, it is a pretty bad metaphor. The circadian clock does not really work like a clock (and some people in the field have always grumbled against the use of the term). Its logic is more similar to a Rube-Goldberg machine. A few years ago my wife bought me a book containing all of the original examples of the Rube-Goldberg machines, but if you have not seen those, I guess you have watched a few episodes of a cartoon like Tom and Jerry in which Tom designs a machine in which one action results in the next and next and next until the last action traps Jerry. Here is an example by Rube Goldberg himself: Golfer pulls trigger shooting tee into ground at far end of a gun. Report of the gun causes a groundhog to run into a hole. Leash on the groundhog's collar pulls on the edge of a platform containing a cannon ball. Cannon ball drops on bulb causing atomizer to spray a shirt. Shirt shrinks, gently opening the attached ice-tongs that are holding a golf ball. Golf ball drops on the tee.

A mammalian circadian clock is like a hugely complicated Rube-Goldberg machine. But you can take away, with very little re-arrangement, piece by piece, all elements of the machine, until you are left with just a single simple switch that turns something on or off - like Tom simply jumping on Jerry, or a golfer simply placing a ball on the tee with his hand, or like a clock in cyanobacteria. This is a very very reducible complexity.


Blogger Chris said...

Great post, Bora. This is really fascinating stuff. Sometimes I feel like I should learn more about the biological aspects of time-representation in humans, since I am doing research on the conceptual representation of time in humans, but then I remember that I'm not at all qualified to evaluate biology reserach, and that while the theory of time representation that I am competing against does treat time representations as embodied, I'm not sure how even they would integrate this sort of stuff. Still, I find it incredibly fascinating.

7:18 PM  
Blogger jamie said...

Excellent response, coturnix, and from a field that, from what I've seen, isn't often at the forefront of the IDC "debate" though it sounds like it should be. I need to remind myself to read this blog, I do keep up w/ you other one. Especially since my circadian clock is broken, apparently, from full time work and school. . .

1:58 AM  
Blogger Suresh said...

Is all of Creation just God's blog?

cool line. I will use it in my .signature (with attribution of course ;))

6:11 PM  
Blogger Henry Holland said...

I too love the "God's blog" line. He is all too redolent of right wingers, though, in that he doesn't have a comments section. I have a few choice remarks I'd like to leave for Him.

Great stuff, btw, thank you for writing it at a non-specialist level so that peasants like me can grasp it.

5:11 PM  
Blogger Canis Ex Machina said...

It can also be noted that the sadly popular creationist Ken Ham's blog does not have comments. A pity - yea verily, he speaketh much bullshit.
Nice blog! Very interesting both as a foil to creationist spiel and also from the point of view of scientific interest.

9:11 AM  
Blogger Apesnake said...

"Obviously, they had to have been programmed initially into all biological life forms by the Creator (Jesus Christ) himself."

I wish someone had asked him how the word obvious was meant here.

1)It was obvious that the creator did the programing as opposed to the creator's lab assistant or his IT support workers.

2) It was obvious that the programing occurred initially as opposed to after the creation of bacteria which lack the clock.

3) It was obvious that the creator is Jesus Christ as opposed to Vishnu, Saint Barnabas or Mr Magoo.

None of these things seem obvious even if you accept the unsupported assumption of intelligent origin for the clock.

The only thing that is obvious is that they do not teach logic in schools.

12:04 PM  

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