MacroEvolution
Convergent Evolution 
Premordial Soup
Gene Duplication
Transition Fossil 
Posted on 05/18/2005 11:23:17 AM PDT by DannyTN
Rotary Clock Discovered in Bacteria
What could be more mechanical than a mechanical clock?
A biochemist has discovered one in the simplest of organisms, one-celled cyanobacteria. Examining the three complex protein components of its circadian clock, he thinks he has hit on a model that explains its structure and function: it rotates to keep time. Though it keeps good time, this clock is only about 10 billionths of a meter tall.
Scientists have known the parts of the cyanobacterial clock. They are named KaiA, KaiB, and KaiC. Jimin Wang of the Department of Molecular Biophysics and Biochemistry at Yale, publishing in Structure,1 has found an elegant solution to how the parts interact. He was inspired by the similarity of these parts to those in ATP synthase (see 04/30/2005 entry), a universal enzyme known as a rotary motor. Though structurally different, the Kai proteins appear to operate as another rotary motor – this time, a clock.
We learned last time (see 09/15/2004 entry) that the parts interact in some way in sync with the diurnal cycle, but the mechanism was still a “black box.” Wang found that the KaiC part, a six-sided hexagonal cylinder, has a central cavity where the KaiA part can fit when it undergoes an “activation” that changes its shape, somewhat like unfolding scissors. Like a key, it fits into the central shaft and turns. The KaiB part, like a wing nut, fastens on KaiB at the bottom of the KaiC carousel. For every 120ö turn of the spindle, phosphate groups attach to the outside of the carousel, till KaiC is fully saturated, or phosphorylated. This apparently happens to multiple Kai complexes during the night.
How does this keep time? When unphosphorylated, KaiC affects the expression of genes. During the night, when complexed with the other two parts, it is repressed from acting, effectively shutting down the cell for the night. Apparently many of these complexes form and dissociate each cycle. As the complexes break up in the morning, expression resumes, and the cell wakes up. When KaiC separates from the other parts, it is destroyed, stopping its repression of genes and stimulating the creation of more KaiC. “In summary,” he says, “the Kai complexes are a rotary clock for phosphorylation, which sets the destruction pace of the night-dominant Kai complexes and timely releases KaiA.” The system sets up a day-night oscillation feedback loop that allows the bacterium keep in sync with the time of day.
Wang shares the surprise that a bacterium could have a clock that persists longer than the cell-division cycle. This means that the act of cell division does not break the clock:
The discovery of a bacterial clock unexpectedly breaks the paradigm of biological clocks, because rapid cell division and chromosome duplication in bacteria occur within one circadian period (Kondo et al., 1994 and Kondo et al., 1997). In fact, these cyanobacterial oscillators in individual cells have a strong temporal stability with a correlation time of several months. (Emphasis added in all quotes.)Wang’s article has elegant diagrams of the parts and how they precisely fit together. In his model, the KaiC carousel resembles the hexagonal F1 motor of ATP synthase, and the KaiA “key” that fits into the central shaft resembles the camshaft. KaiB, in turn, acts like the inhibitor in ATP synthase. “The close relationship between the two systems may well extend beyond their structural similarity,” he suggests in conclusion, “because the rhythmic photosynthesis-dependent ATP generation is an important process under the Kai circadian regulation.”
Need we tell readers what we are about to say? “There is no mention of evolution in this paper.” The inverse law of Darwinese stands: the more detailed the discussion of cellular complexity, the less the tendency to mention evolution.
This is wonderful stuff. The cell is alive with wheels, gears, motors, monorails, winches, ratchets and clocks. Paley would be pleased.
Either that or A LOOKUP TABLE IN YER HEAD.
(ANYone want to buy a used CAPSLOCK key?)
Then they need to read "Tiling the Plane" for a bit of diversity in their busy, humdrum lives.
Just HOW do you KNOW this information?
As a diversion, go to the park with a friend and some tennis balls.
Get on the rotary spinning wheel thingy (merry-go-round?), sitting directly opposite each other.
Spin the wheel at a good pace, and gently toss the balls between one another.
I will try this one more time. First of all, I do NOT believe bees can do calculus. That is kind of my whole point. Second, your comparison would work if you presented it like this:
You tell me that you are going to throw a ball to me. You tell me the starting height, the angle, the force, wind speed, etc. Then you ask me to place my hand where I think the ball will be so I can catch it but you add the requirement that once I position my hand, I can't move it. If I knew calculus, I could calculate the position fairly accurately and place my hand in the right spot to catch the ball.
That is, essentially, what we are asking the bees to do. We know, a priori, what the displacement has to be in order to minimize surface area (i.e. bee's wax) when constructing the pointy end of the honeycomb. (That's like the placement of the hand in the throwing example.) Then the bees start building and, low and behold, the displacement they build in to the pointy end matches the value we came up with that minimizes the wax used. And, no, bees can't do calculus. That's the WHOLE POINT.
Really, I don't know it. That is why sometimes I drop or miss the ball. Also, the first place I put my hand when the ball is thrown is likely not the final placement when the ball is caught. The position is adjusted, a posterior, based on what I am seeing. To claim the bees are making building decisions in terms of the displacement used, a posterior, would be to imply they are actually doing calculus. Clearly, that is not the case. That is the difference.
So what exactly is your point? When the behavior of bees and termites and birds building nests has been carefully investigated the rules for their construction behavior turn out to be very simple and involve no knowledge or calculations.
You are not going to like my answer so let me ask you a question instead.
Did we invent or discover mathematics? That is the fundamental question.
That is one of those pseudo-questions like, do you believe in free-will or determinism. Good for keeping college kids awake at night, but leading nowhere.
For the record, I lean toward invention for axioms and discovery for the implications of the axioms.
I disagree. It is a fundamental origins question.
For the record, I lean toward invention for axioms and discovery for the implications of the axioms.
Your belief has some problems. Historically, secular mathematicians have agreed that we should have absolutely no expectation that our invented axioms would have any application in the real world. The fact that over and over again they do is what Einstein referred to as a "miracle".
Just like my vintage 2002 CD player - it's still flashing "1200". I guess it's 12 noon somewhere.
Axioms are selected because they are effective in the real world. But when the boundaries of the real world expand due to experience, the axioms begin to fray at the edges.
We cannot imagine violations of the fundamental axioms of arithmetic because we have no experience with exceptions. Arithmetic is an extension of counting, and we do not experience anomolies in the process of counting.
We have experienced anomolies in geometry, leading to adjustments in the axioms of geometry. Imagine trying to explain to the ancient Greeks that the geometry of relativity describes the real world.
So that's where my watch evolved from, and all the time I thought it was made by Timex.
You make mathematics sound like a dart-board approach. Throw out everything and keep what sticks. In my experience, that is not how mathematics is developed. But, anyway, such a posterior axioms are not what I am talking about.
Where the heart of the matter lies is in two areas. First, in purely theoretical mathematics and physics and, second, in very small or invisible natural processes that we have been able to describe mathematically before we could observe them.
In the first case, effectiveness in the real world is not a consideration because the axioms are developed in the purely theoretical realm. In the second case, effectiveness in the real world is not a consideration because it was only later, after the development of the axioms, that their effectiveness in describing the real world was realized once we had developed the technology to test them.
Now, lest you propose that a whole bunch of axioms are developed and tested and we keep the ones that work, I will relate to you this story to show that, actually, the opposite is true.
There was a mathetician in the 20th century who found the whole idea that mathematics is discovered so offensive that he purposely set out to develop theoretical mathematics that would have no application in the real world. After his death, his work turned out to be useful in genetics and in the study of temperatures in smelting furnaces.
MacroEvolution
Convergent Evolution
Premordial Soup
Gene Duplication
Transition Fossil
and then there spider webs....
Yeah....
Everywhere along W30° 9' 47"
I
Daylight savings time!
Question for the hour:
How can we tell that mechanical dial clocks were invented in the Northern hemisphere?
If a bacterium can have a clock, a bee could easily have a miniature computer. I've heard they like Apples.
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