** Horrendous Complexity **Let us now zoom in to watch these protein machines performing. Viewed down a light microscope at a few hundred times magnification as was in Darwin's day, the cell was a boring spectacle. It appeared only as a disorderly blob of goo which would shift around here and there randomly. But as our understanding grew, and new technologies such as the electron microscope emerged, the spectacle turned out to contain machines performing, well.. let's just say better than the Moscow State Circus.
a glimpse into the underlying world of microbiology
a glimpse into the underlying world of microbiology
Here is a simplified overview given by Biochemistry Professor Michael Behe of Lehigh University regarding the first stage of how light is transformed to an electrical signal in the human eye  (we prepared a version with commentaries which is available here). Please fasten your seatbelts and keep your arms inside the vehicle:
When light strikes the retina a photon is absorbed (through a quantum mechanical process) by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds (10^-12 seconds) to trans-retinal.Interesting little world, don't you think? The above-mentioned example is not only for vision of the eye. Just about every system in living creatures exhibits this kind of circus of complexity and even more when examined at the level of biochemistry.
The change in shape of 11-cis-retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound.
As a consequence of the [rhodopsin] protein's metamorphosis, the behavior of the protein changes in a very specific way. The altered [rhodopsin] protein can now interact with another protein called transducin.
Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin.
The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP.
Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water.
A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range.
When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision.
If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state.
There are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration.
However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration.
Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall.
Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate.
The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon.
Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle.
To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol.
Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete...
Other examples of irreducible complexity abound, including aspects of protein transport, blood clotting, closed circular DNA, electron transport, telomeres, photosynthesis, transcription regulation, and much more...
source: www.arn.org/docs/behe/mb_mm92496.htm see there for more
The big picture, or system view of the eye is also an interesting story.
As light enters your eye, about seven million cone-shaped color sensors automatically fine tune your color contrast and detail vision depending on the lighting conditions. Whenever there isn't enough light for an accurate color picture, the cone-shaped sensors sign off and about 125 million rod-shaped, ultra-sensitive black and white sensors switch in. Meanwhile a processor in your optic nerve receives signals from those 125 million sensors, recodes them, and zaps them down a few hundred thousand nerve fibers leading to your brain at about one billion pulses per second.
While all this is going on, the pupil is monitoring and maintaining the level of light within your eye, a stereo focusing system is maintaining maximum image sharpness and a sophisticated image enhancer is clarifying tiny blurs in your vision caused by motion or darkness. (from Eye of the Needle pg.195)
Let us note that according to scientists complex, image-forming eyes "evolved" independently some 50 to 100 times  - i.e. there are at least 50 independent lines of animals, spiders, jellyfish and who knows what, all of which have "evolved" complex, image-forming eyes. Many of these are highly exotic and far more advanced than human eyes.
The eye also requires coordination with the brain, such as flipping images properly and putting things in context. Babies for example can see but they can't yet put things in context. This necessitates cognitive powers to interpret the information from the eye and put them into proper context. There is much to study.
Dr. Douglas Borchman, a professor of Opthamology at the University of Louisville studied the lens of the human eye for decades and says there is still so much more to learn. He notes:
"I'm in awe of some of the things I see. It's too beautiful. Every day I go to work to unlock the mystery of the eye. The cornea, lens, retina, nerves, connections are ridiculously complex. There is so much to know. For an eye to be able to see, all the basic components must be present at the same time and work together perfectly. For instance, if all the other components, such as the cornea, iris, pupil, retina, tear glands, and eye muscles, are all present and functioning properly, but just the eyelid is missing, then the eye will incur serious damage, dry up and blindness would quickly ensue.".Let us now examine a minor component of the human eye - the eyelid.
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