origin of light-sensitivity (The atheist delusion)

by George Jelliss ⌂ @, Crewe, Thursday, January 24, 2008, 19:41 (6146 days ago)
edited by unknown, Thursday, January 24, 2008, 19:49

I've been trying to find links to an article that explains the latest scientific views on this, but most of them require subscription to journals and are in highly technical language. The best I've found so far that are accessible to the general reader are these two: - The first is a long article on the evolution of eyes by Kenneth Miller (who is an evolutionary biologist and also a theist - he gave evidence at the Dover trial, against ID): - http://www.pbs.org/wgbh/evolution/change/grand/ - The second is an account by a biochemist of Vitamin A (which because of its connection with sight is also known as "retinol"): - http://sandwalk.blogspot.com/2007/08/vitamin-retinol.html - Thus the origin of a "light-sensitive spot" is just a matter of a slight change in the structure of a chemical compound. - The above was in response to the phrase "... out of the blue developed sensitivity to light (= sight), ..." which occurs on this page.

origin of light-sensitivity

by dhw, Friday, January 25, 2008, 16:54 (6145 days ago) @ George Jelliss

As always, you are a mine of information. The item about the eye was enlightening in more senses than one, with an interesting sting in the tail. The problem with ID is that it's such a useful term, but it's hard to separate it from all its religious associations when you're trying to look at the situation from a neutral standpoint. - I'm afraid I shall need to eat a lot more carrots before I can cope with the other article!

origin of light-sensitivity

by George Jelliss ⌂ @, Crewe, Sunday, January 27, 2008, 16:13 (6143 days ago) @ dhw

You write: "I'm afraid I shall need to eat a lot more carrots before I can cope with the other article!" But there is very little to "cope" with there but basic chemistry. You cannot possibly hope to understand modern biology without at least a basic understanding of chemistry. - In chapter 3, on Evolution, you have "In this context of physical change, natural selection explains nothing, because although it tells us why beneficial changes survive and are perpetuated, and indeed why organs will improve over time, it does not explain the mechanism that enables such changes to take place." and: "The miracle lies in the original, primitive, light-sensitive "nerve", which if it did not already provide some degree of advantage ... even 0.0001% of human vision ... would not have survived. This may have been "simple" by comparison with later eyes, but it remains inexplicable." - But it is not a miracle nor is it inexplicable. It is explained by an understanding of the biochemistry within cells. This is of course something that we have developed since Darwin's day. Darwin, as you have shown in several quotes, was not able to say exactly how a light-sensitive spot might develop, and confined his theory to how natural selection would act to preserve such an advantageous variation. But now we can say how such a change could occur. - Most biochemistry only involves the elements H, C, N, O (with others occasionally) and mostly involves chains of carbon atoms (C) with hydrogen atoms (H) attached to the unused bonds. That's what the lines of bonds in the diagrams are a shorthand for. It's not that difficult to comprehend.

origin of light-sensitivity

by dhw, Tuesday, January 29, 2008, 07:58 (6142 days ago) @ George Jelliss

I shan't pretend that I can enter into a discussion on biochemistry with you, but I am struggling to follow some of the reasoning. - Firstly, the 'carrot' website said nothing about the origin of light sensitivity. "The aldehyde retinal is a light sensitive compound with an important role in vision. Retinal is the prosthetic group of the protein rhodopsin; absorption of a photon of light by retinal triggers a neural impulse." This was the only reference I found to vision. - I stand by my first statement that natural selection does not explain physical change and does not explain the mechanism that enables such changes to take place. Natural selection is only part of the process of evolution and explains why changes are perpetuated. - With regard to my second statement, I am not denying that what in your first posting you called "a slight change" took place. But the fact that modern science can now tell us what it was that changed does not provide us with an explanation of why that change was able to take place. - If all biochemists agreed that chance was bound to create the mechanism which brought about changes leading to hitherto unheard-of concepts like sight, taste, sex, consciousness etc., I would gladly throw my doubts out of the window and join you in your atheism. Interestingly, the website dealing with the origin of light sensitivity to which you kindly drew my attention was written by a cell biologist, Professor Kenneth Miller. He concludes: "The living world is filled with examples of many other organs and structures that clearly have their roots in the opportunistic modification of a preexisting structure rather than the clean elegance of design. This does not, however, despite the fears of "intelligent design" advocates, amount to evidence against the existence of a Deity. Properly understood, as Darwin himself pointed out, it only deepens our respect for the power and subtlety of the Creator's remarkable ways." - I am not a chemist, I am not a biologist, I am not a theist, and I am not an atheist, so I'd rather you fought it out with Professor Miller than with me.

origin of light-sensitivity

by whitecraw, Friday, February 01, 2008, 10:23 (6139 days ago) @ dhw

'I stand by my first statement that natural selection does not explain physical change and does not explain the mechanism that enables such changes to take place. Natural selection is only part of the process of evolution and explains why changes are perpetuated.' - You're right. The natural selection bit of the theory of evolution by natural selection only explains how particular physical characteristics come to predominate in populations; it does not explain how variation in physical characteristics within a population occurs. It's the biochemistry bit of the theory that does this. The physical changes that lead to variation within a population occur as a result of changes in a DNA sequence, usually occurring because of errors in replication or repair. According to the theory, random mutation at the genetic level is the ultimate source of the physical changes that give rise to variations in physical characteristics within a population, which either survive in or die out in a population depending on whether or not they are disadvantageous to the bearers of those characteristics in the competition to live and reproduce.

origin of light-sensitivity

by David Turell @, Monday, December 01, 2008, 14:00 (5835 days ago) @ George Jelliss

Thus the origin of a "light-sensitive spot" is just a matter of a slight change in the structure of a chemical compound.
 
> The above was in response to the phrase "... out of the blue developed sensitivity to light (= sight), ..." which occurs on this page. > - The development of sight has resulted in at least 5-6 types of eyes, part of the evidence for Simon Conway Morris' 'convergence' approach to evolution, implying that certain developments are inevitable. Enjoy these slides: http://www.nature.com/news/specials/darwin/gallery/index.html

origin of light-sensitivity: C elegans cell senses light

by David Turell @, Tuesday, November 22, 2016, 00:59 (2922 days ago) @ David Turell

C. elegans is a very simple worm, in which a light-sensitive cell has been found:

http://www.livescience.com/56913-new-photoreceptor-found-in-worms.html

"An international team of researchers found the photoreceptor, called LITE-1, in the millimeter-long nematode Caenorhabditis elegans, a model animal that scientists often use in research. The finding is a remarkable one, they said, as it's only the third type of photoreceptor to be identified in animals. (The other two are opsins and cryptochromes, they said.)

***

"An earlier study published by Xu and his colleagues showed that although nematodes have no eyes, they still move away from flashes of light. The new study suggests why: Instead of serving as an intermediary that senses chemicals formed by light reactions, LITE-1 absorbs light directly, "indicating that LITE-1 is highly efficient in capturing photons," they wrote in the study.

"'Photoreceptors convert light into a signal that the body can use," Xu said. "LITE-1 is unusual in that it is extremely efficient at absorbing both UV-A and UV-B light — 10 to 100 times greater than the two other types found in the animal kingdom: opsins and cryptochromes. The next step is to better understand why it has these amazing properties."

"After analyzing LITE-1's genetic code, the researchers realized that it was extremely different from photoreceptors found in plants, animals and microbes, Xu said.

Moreover, LITE-1 has several unique features. In animals, photoreceptors usually have two components: a base protein and a chromophore (a light-absorbing compound). If these two components are broken apart, the chromophore is still able to work, though not as well, the researchers said.

"In contrast, LITE-1 can't absorb light if its two components split up, Xu said.
In addition, the team found that LITE-1 is dependent on the amino acid tryptophan, which is present in two different places within it. To test this, researchers added a modified GUR-3, a nonlight-sensitive protein in the same family, to the tryptophan residues. However, GUR-3 only had about a third of the sensitivity to UV-B as LITE-1 did, they found."

Comment: Light sensitivity had to start somehow during evolution. It is hard to imagine C elegans stumbled upon this complex molecule by chance. Still it is a giant jump from this type of non-descript sensitivity to Cambrian animal eyes, which appeared with no precursors. No wonder Darwin was so afraid of the Cambrian Explosion and was sure stepwise forms would be found. They haven't been and the gap just gets wider and wider in their absence since the preceeding Ediacaran fossils have been well displayed with no eyes showing.

origin of light-sensitivity: sensors are everywhere

by David Turell @, Tuesday, September 05, 2017, 21:42 (2634 days ago) @ David Turell

It seems organisms have light-sensing molecules everywhere:

https://cosmosmagazine.com/biology/seeing-without-eyes-the-unexpected-world-of-nonvisua...

"But scientists have discovered in recent decades that many animals – including human beings – do have specialized light-detecting molecules in unexpected places, outside of the eyes. These “extraocular photoreceptors” are usually found in the central nervous system or in the skin, but also frequently in internal organs. What are light-sensing molecules doing in places beyond the eyes?

"All the visual cells identified in animals detect light using a single family of proteins, called the opsins. These proteins grab a light-sensitive molecule – derived from vitamin A – that changes its structure when exposed to light. The opsin in turn changes its own shape and turns on signaling pathways in photoreceptor cells that ultimately send a message to the brain that light has been detected.

***

"The photoreceptors scientists have found beyond the eyes are most commonly located in the central nervous system. Almost all animals have several types in the brain and often in the nerves as well.

"The skin is where we see most other light receptors, particularly in active color-changing cells or skin organs called chromatophores. These are the black, brown or brightly colored spots sported by many fish, crabs or frogs. They reach their highest development in the cephalopods: octopus, squid and cuttlefish. Animals actively control their color or pattern for several reasons, most often for camouflage (to match the color and pattern of the background) or to produce bright, prominent signals for aggression or attracting a mate.

"Surprisingly, there is a second class of light-sensitive molecules besides the opsins, never used for vision (as far as we know). They show up in some nervous structures, such as the brains or antennae of some insects and even in bird retinas. These are the cryptochromes, well-named because their functions and methods of action are still poorly understood. Cryptochromes were originally discovered in plants, where they control growth and annual reproductive changes.

"Now that we know that these photoreceptors can be found throughout animals’ bodies, what in the world are they actually doing? Obviously, their function depends in part on their location.

"Generally, they regulate light-mediated behavior that exists below the level of consciousness and that doesn’t require having an extremely precise knowledge of a light source’s location in space or time. Typical functions include the timing of daily cycles of alertness, sleep and wake, mood, body temperature and numerous other internal cycles that are synchronized to the changes of day and night.

"Biological clocks that maintain regular physiological cycles – and cause the discomforts of jet lag – nearly always are controlled by these photoreceptors. These detectors are also important for the opening and closing of the eye’s pupil to help adjust to varying light levels. Skin photoreceptors like those in fish or octopus often control color and pattern variations.

"In some animals, they have a quite different, and rather amazing, task – providing magnetoreception, the ability to detect the Earth’s magnetic field. This capacity is based on the cryptochromes, which apparently underlie mechanisms for magnetic orientation in animals as different as birds and cockroaches.

***

"Finally, an unexpected recent finding in research led by Solomon Snyder and Dan Berkowitz, also at Johns Hopkins University, found that blood vessels in mice contain melanopsin, the opsin used in retinal nonvisual photoreception. They found that this light-sensitive protein can regulate blood vessels’ contraction and relaxation. Since humans are likely to have the same system, this could partially explain the increase in heart attacks in the morning, which are perhaps associated with blood pressure changes occurring at that time."

Comment: This article suggests that development of light sensitivity and then vision was a major drive of the evolutionary process. From fish to insects to primates helpful vision is primary to advanced functions.

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