[_ Old Earth _] A number reasons why I find Evolution impossible to believe!

[Barbarian]

I wonder how does anyone know the variation they see is transitional?

If it has homologies that are intermediate between at least two other forms, it's transitional by definition. You don't need to assume evolution. Evolution is the conclusion, not the evidence. Transitionals are the evidence.

I see many scientists accept evolution yet recognize the difference between what can be known, and what is inferred,

All knowledge in science is inferred. We can't get logical certainty in science. This might seem a bit shaky to you, but I can only point out that science has been spectacularly successful at understanding the world around us.

thus they say "this suggests, or we believe, or could be or might be". If there is a new discovery it will have to be accounted for and adjustments will be made. Transitional is an inference based on observations.

Yep. That's science. We make inferences from evidence.

Barbarian suggests:
We should use the scientific definition. (a hypothesis is) A proposed and testable explanation for a natural phenomenon.

I agree.

 

[Milk-Drops]

I wonder how does anyone know the variation they see is transitional? They would have to know, not infer, the original form. They would have to know, not infer, every stage was linked. I see many scientists accept evolution yet recognize the difference between what can be known, and what is inferred, thus they say "this suggests, or we believe, or could be or might be". If there is a new discovery it will have to be accounted for and adjustments will be made. Transitional is an inference based on observations.

When discussing transitional forms, what needs to be noted is that there is a starting point and an end point in phylogeny when tracking lineages.

For instance the theory of Evolution by Darwin states that organisms diverge based on the modifications through decent. This is observed in the wild with documentations of Ring Species, punctuated equilibrium, The bottle neck effect, selective breeding, etc.

So there is reason to hypothesis that organisms can be traced back genetically to find where specif adaptations arise. Now I understand that a popular saying is a dog is always a dog and it will only produce more dogs. That is actually true. However we can see where the dog species came from.

Humans have documented the domestication of Wolves to breed dogs. From there we can see where the whole branch of Dogs spanned through human breeding depending on the area they where bred and for what purpose. With This we can see the connection of species. With this information we can track back the group Canis and find Foxes, Coyotes, and Wolves, are all related genetically. When looking for transitions, it is the hypothesis that we should find what is believed to be the transition around the time of the emergence of the current species. Geneticly Wolves, Foxes, Yotes, and dogs all fall into Canidae. So all of those animals can be nothing but Canidae. Canidae split off in one direction in the group of Caniforms, which is from the Order of Carnivores. The other split would from the groups Muslidae ( Weasils), Ursidae ( Bears, Wolverines), Pryoconidae ( Racoons, Red Pandas), and another group I'm not even going to try and spell that includes walruses, seals, and sea lions.

Now, when looking for a transition, both the genetics and the homology are combined to see where the now extinct species would fit. With homology we can nail down the adaptations, and with genetics we can set up where the organisms fits within all the other organisms.

Page 12 of this Paper is pretty nifty. http://www.canids.org/cap/CANID1.pdf

Any questions so far?

 

[Vaccine]

If it has homologies that are intermediate between at least two other forms, it's transitional by definition.

The relationship between those two other forms is inferred not known.

All knowledge in science is inferred.

One might say that about evolution, but those spectacular successes are based on facts. They manufacture medicine, computers, radios, airplanes, build bridges, perform surgeries a long list of other things based on what is known, not inferred.

Barbarian observes:
A bit of dark pigment allows a cell to become more sensitive to light.

What allows a cell to be sensitive to light is the 11-cis-retinal protein

Barbarian replied-In some highly-evolved organisms. But as you just saw, all that's really necessary is a darker pigment like meletonin,

Melatonin is a hormone, perhaps you meant melanin?
No sarcasm intended but telling me a dark pigment allows a cell to sense light is similar to saying pushing a button on a radio allows a station to be received. While that may be true in general, it is not very accurate. In order to discuss the origin of a light sensitive cell we need to break it down more.
An organ can be broken down to tissue, tissue broken down to cells. What allows a cell to sense light is a receptor in the cell membrane called an opsin. The actual part of an opsin that reacts to a photon is the 11-cis-retinal protein. Other isotopes of 11-cis are also chromophores but only 11-cis is part of a visual chromophore, and not just in some "highly-evolved" organisms but all animals.

Heat maybe, Not light.

No, it's light. You see, visible light, impacting a dark object, is absorbed by the object and transformed to heat, which is easily detected by an organsm. So, the simplest light sensitive sell is just a cell with extra pigment. The simplest known photopigment is melatonin, sensitive because its darker

Melatonin is a hormone, so I'll assume you meant melanopsin. Melanopsin is another type of opsin which functions by binding to 11-cis-retinal. 11-cis-retinal IS a chromophore(pigment). What allows a cell to detect heat is TRPV3 protein, but detecting heat is off topic.

What allows it to sense heat is the transient receptor potential cation channel, subfamily V protein, specifically TRPV3

Bacteria and protists like Euglena detect light and heat and usefully respond to it, without any of that

Of course they don't use TRPV3, but they do have opsins. Which use 13-cis-retinal, an isotope of 11-cis-retinal, and all-trans-retinal to sense light. Since there is no evidence eukaryotic opsins evolved from prokaryotic opsins I fail to see the relavence.

You've gone a bit off the path, here. The evidence is that the simplest photosensitive pigment is merely a dark substance that allows light to be transformed to thermal energy

No, really, I haven't gone off the path. I hate to point this out but that dark "substance" has been the topic of my posts. 11-cis is a chromophore(pigment).

However, any gene sequences between TRPV3 and 11-cis-retinal would be invisible to natural selection

However, as you see, a gene that caused a dark pigment to collect in a cell would make it more sensitive to light, and thereby more useful to the organism

That argument seems to be based on the premise a cell senses heat/light the same way. Science has learned there are different proteins associate with those functions. Even the article you cited began with an opsin. However, I have several issues with that article.
1. Placozoan do not have true opsins.
2. Unless one uses evolution to prove evolution:
"placozoan sequences are, from an evolutionary point of view, true opsins(irrespective of their function)."
http://mcidublin.conference-service...tract.xsl&conferenceID=2905&abstractID=628855
3. It was an inference of its amino acid sequence suggests that this protein might not have been light-sensitive.

Also, that article said nothing whatever about the origin or possible molecular evolution of 11-cis-retinal, the actual protein that is sensitive to light

As you see, there are much simpler molecules sensitive to light.

I see 11-cis-retinal is part of a visual molecule, with no explanation of an origin or possible molecular evolution.

 

[Vaccine]

Any questions so far?

Not really. I was trying to avoid ad hominem argument about what is fact and what is inferred.

Fact: A thing that is indisputably the case

... But you'll surely agree that those transitional forms are a fact; they still exist in living organisms today.

Not a true/false issue, just sayin' it's an inference.

 

[Milk-Drops]

Not really. I was trying to avoid ad hominem argument about what is fact and what is inferred.

I was just sharing how Phylogeny uses the term transitional. That is all.

 

[Barbarian]

Barbarian observes:
If it has homologies that are intermediate between at least two other forms, it's transitional by definition.

The relationship between those two other forms is inferred not known.

As you see, the fact that an organism is transitional relative to two others, does not depend on an assumption of evolution. They are measurably transitional. The only issue is how you can reasonably explain it.

All knowledge in science is inferred.

One might say that about evolution,

It's true of all science.

but those spectacular successes are based on facts.

Of course. When Hall observed the evolution of a new, irreducibly complex enzyme system in bacteria, those were observed facts. The inference is that mutation and natural selection can produce useful new features.

They manufacture medicine, computers, radios, airplanes, build bridges, perform surgeries a long list of other things based on what is known, not inferred.

What we know in science is from inferences. No one logically proved atoms. No one logically proved anything in science. Learn about it here:

Scientific theories are never proven completely. They are supported by facts, but they never become (ultimate, unchangeable) facts. As Carroll writes, we have to take “I believe x†to mean, not “I can prove x is the caseâ€, but “it would be unreasonable to doubt x.†The absence of a reasonable doubt (based on evidences) is what makes a scientific theory “trueâ€.
http://vishal12.wordpress.com/2009/08/17/science-never-proves-anything/

If you don't get this, you don't get science.

Barbarian observes:
A bit of dark pigment allows a cell to become more sensitive to light.

What allows a cell to be sensitive to light is the 11-cis-retinal protein

Barbarian observes:

In some highly-evolved organisms. But as you just saw, all that's really necessary is a darker pigment like meletonin,

Melatonin is a hormone, perhaps you meant melanin?

Metazoan opsin evolution reveals a simple route to animal vision
Proceedings of the National Academy of Science of the United States
PNAS October 29, 2012
All known visual pigments in Neuralia (Cnidaria, Ctenophora, and Bilateria) are composed of an opsin (a seven-transmembrane G protein-coupled receptor), and a light-sensitive chromophore, generally retinal. Accordingly, opsins play a key role in vision. There is no agreement on the relationships of the neuralian opsin subfamilies, and clarifying their phylogeny is key to elucidating the origin of this protein family and of vision. We used improved methods and data to resolve the opsin phylogeny and explain the evolution of animal vision. We found that the Placozoa have opsins, and that the opsins share a common ancestor with the melatonin receptors.

No sarcasm intended but telling me a dark pigment allows a cell to sense light is similar to saying pushing a button on a radio allows a station to be received.

The difference, of course, is that in the case of the dark spot, the spot is the directly receptor, and of course, in the radio, the button is not. As you see, those highly-evolved molecules don't even exist in many organisms that can detect light and make use of that perception.

In order to discuss the origin of a light sensitive cell we need to break it down more.

So tell me about light-detecting bacteria. How does that work, without the highly-evolved molecules you think are essential to vision?

An organ can be broken down to tissue, tissue broken down to cells. What allows a cell to sense light is a receptor in the cell membrane called an opsin.

What about bacteria that lack them, but still react usefully to light? They don't have opsins, but they have very primitive molecules called "rhodopsins" that work well enough. The protists, like Euglena, have pigments that are transitional between the very simple bacterial forms, and the complex forms in vertebrates.

Behe’s core claim is that if a modern system breaks when you remove a part, then you can’t build that system by incremental evolutionary steps. For example, he would claim that a photopigment without any linkers or down stream signalling molecules would be useless, and unselectable by natural selection. Really?

One of the iconic light spots is that of the eukaryotic single-celled organism Euglena. The Euglena signal transduction cascade consists of a single protein, the light harvesting protein and the protein that generates the single signaling molecule is one and the same (Iseki et al., 2002). This is a simple “one step†cascade that is eminently evolvable.

However, the photopigments of vertebrates and inverebrates isn’t closely related to the light harvesting pigment of Euglena. In fact they are a member of a family of ancient proteins, the rhodopsins. Rhodopsins are seven transmembrane domain proteins, and are present in bacteria (Bacteriorhodopsin) and eukaryotic algae (Volvox and Chlamydia) as well as invertebrates and vertebrates.

ID apologists aren’t known for generating testable hypotheses, and generally ordinary scientists have to do it for them. This case is no exception, as the above information suggests an experiment. If Behe is right, then putting a microbial rhodopsin, which doesn’t uses vertebrate visual signal transduction pathways, into an ordinary vertebrate neuron, which doesn’t have the vertebrate visual signalling pathway, should do absolutely nothing. Well, Bi et al (2006) did that experiment (but for reasons totally unrelated to ID).

In certain diseases the photoreceptors degenerate. However, the supporting retinal ganglion cells, which pass on the nerve impulses from the photoreceptors to the brain, often remain intact. These retinal ganglion cells are not light sensitive. Bi and colleagues used a mouse model of photoreceptor degeneration. As the mouse ages, it progressively loses photoreceptors (and vision). When all the photoreceptors had gone, and the retinas of the mice no longer responded to light, the researchers transfected the retinal ganglion cells (with no visual transduction pathway remember), with the microbial rhodopsin (which doesn’t link to the vertebrate pathways anyway).

And visual responses were restored. The ganglion cells transfected with the microbial rhodopsin responded to light, depolarised and passed signals on to the visual cortex (Bi et al., 2006). They are not quite as effective as photoreceptors, as the retinal ganglion cells do not have the stacked membranes of the photoreceptors that increase light harvesting efficiency, nor the amplification of the vertebrate signal transduction cascade. But they do work. It’s not just mice, other researchers have transfected these receptors into non-photosensitive nerves in worms, and they become light sensitive and moved away from the light (Nagel et al. 2005).

So Behe is wrong.
http://pandasthumb.org/archives/2006/11/blind-mice-vs-b.html

The actual part of an opsin that reacts to a photon is the 11-cis-retinal protein. Other isotopes of 11-cis are also chromophores but only 11-cis is part of a visual chromophore, and not just in some "highly-evolved" organisms but all animals.

Notice that primitive organisms don't have these features. See above.

(Barbarian notes that a simple dark spot can make a cell more sensitive to light)

Heat maybe, Not light.

No, it's light. You see, visible light, impacting a dark object, is absorbed by the object and transformed to heat, which is easily detected by an organsm. So, the simplest light sensitive sell is just a cell with extra pigment. The simplest known photopigment is melatonin, sensitive because its darker

Melatonin is a hormone, so I'll assume you meant melanopsin.

See the research above. A simple dark receptor can detect light by absorbing it, transforming it to thermal energy, which the organism can then respond usefully. This is the simplest form of vision.

What allows it to sense heat is the transient receptor potential cation channel, subfamily V protein, specifically TRPV3

Bacteria and protists like Euglena detect light and heat and usefully respond to it, without any of that

Of course they don't use TRPV3, but they do have opsins.

Nope. They use a much simpler system, rhodopsins. And protists use some thing transitional between rhodopsins and opsins.

Since there is no evidence eukaryotic opsins evolved from prokaryotic opsins I fail to see the relavence.

Light-Sensing Protein Illuminates Sun-Loving Ocean Bacteria
PLoS Biol. 2005 August; 3(8): e287.
The presence of rhodopsin-like proteins in a wide range of life may eventually provide hints to the protein's evolutionary age. That this large class of transmembrane proteins was so well-conserved over a long evolutionary time scale provides evidence for complex ancient proteins. Another question that remains is whether the proteorhodopsin has any sensory function as does rhodopsin in humans, or whether the bacteria use the protein purely for energy transduction. ​

So, as you see, the evidence indicates that the evolutionary ancestors of opsins were used as photosynthetic molecules, and only later evolved as light sensors. Obviously, it isn't much of a jump from a molecule that can absorb and use light to make a chemical reaction go, to a molecule that can use light to make chemical reaction stimulate a neuron.

You've gone a bit off the path, here. The evidence is that the simplest photosensitive pigment is merely a dark substance that allows light to be transformed to thermal energy

No, really, I haven't gone off the path.

As you now realize, a simple black spot would be adequate for light sensing.

I hate to point this out but that dark "substance" has been the topic of my posts. 11-cis is a chromophore(pigment).

Turns out, the precursors to this are much, much simpler.

However, as you see, a gene that caused a dark pigment to collect in a cell would make it more sensitive to light, and thereby more useful to the organism

That argument seems to be based on the premise a cell senses heat/light the same way.

No. It merely acknowledges that light sensing can be very simple, indeed.

However, I have several issues with that article.
1. Placozoan do not have true opsins.

As you see, very primitive precursors do exist in microbes, and it appears that they began as photosynthetic pigments.

Also, that article said nothing whatever about the origin or possible molecular evolution of 11-cis-retinal, the actual protein that is sensitive to light

As you see, much, much simpler molecules are usefully sensitive to light.

I see 11-cis-retinal is part of a visual molecule, with no explanation of an origin or possible molecular evolution.

See above. It's always like that. Evolution never makes anything de novo; it's always a modification of something already there.

 

[Vaccine]

Not really. I was trying to avoid ad hominem argument about what is fact and what is inferred.

I was just sharing how Phylogeny uses the term transitional. That is all.

Ah, thanks for that. I should add, I think scientists are honest and generally know they are doing. Even if some of it has to be inferred, I don't think they're just pulling this stuff out of nowhere.

 

[Barbarian]

"Model of the energy generating mechanism in marine bacteria. When sunlight strikes a rhodopsin molecule (1), it changes its configuration such that a proton is expelled from the cell (2). The chemical potential causes the proton to flow back into the cell (3), thus generating energy (4) in the form of adenosine triphosphate (5)."

This is a surprisingly simple and primitive phosphorylation mechanism, (phosphorylation is the basis of energy production in all cells). There's more...


The evolution of vision
Advanced Review
Walter J. Gehring
Developmental Biology Dec 21 2012
In this review, the evolution of vision is retraced from its putative origins in cyanobacteria to humans. Circadian oscillatory clocks, phototropism, and phototaxis require the capability to detect light. Photosensory proteins allow us to reconstruct molecular phylogenetic trees. The evolution of animal eyes leading from an ancestral prototype to highly complex image forming eyes can be deciphered on the basis of evolutionary developmental genetic experiments and comparative genomics. As all bilaterian animals share the same master control gene, Pax6, and the same retinal and pigment cell determination genes, we conclude that the different eye‐types originated monophyletically and subsequently diversified by divergent, parallel, or convergent evolution. WIREs Dev Biol 2011 DOI: 10.1002/wdev.96

Some of these heterotrophs have evolved highly complex photoreceptor
structures, resembling a human eye with “cornea”, “lens”, “retina” and “pigment cup”, all in a single cell. During cell division, these “ocelloids” arise from thylakoid membranes, suggesting that they are derived from the chloro-
plast. The dinoflagellate Pyrocystis does indeed contain a proteorhodopsin which is very similar to that of cyanobacteria. Also, in flagellates like Chlamydomonas and Volvox the “eye spot” (ocelloid) is located in the chloroplast, suggesting that the photoreceptors of flagellates and metazoan
might originate from cyanobacteria. These considerations lead to the proposal of a “Russian Doll” hypothesis which assumes that photoreception originated in cyanobacteria and was transferred in at least two symbiotic steps to dino-
flagellates

So we see that primitive photosynthetic proteins are closely associate with light sensitivity in protists.

 

[Vaccine]

No one logically proved anything in science.

Good evening Barbarian! I have to say I don't think it's a good idea to grade all science on a curve, it only drags down the rest of science.

Learn about it here:
Scientific theories are never proven completely. They are supported by facts, but they never become (ultimate, unchangeable) facts. As Carroll writes, we have to take “I believe x” to mean, not “I can prove x is the case”, but “it would be unreasonable to doubt x.” The absence of a reasonable doubt (based on evidences) is what makes a scientific theory “true”.
http://vishal12.wordpress.com/2009/08/17/science-never-proves-anything/

If you don't get this, you don't get science.

When someone puts it that way, it seems I have no choice but to agree with that. However, that last sentence is a subtle attack on truth. In spite of that bullying tactic, I strongly disagree with that. If a theory were "true", it would be called a law or a fact. The absence of a reasonable doubt is what makes a scientific theory convincing. What makes something in science true is when it acquires the status of a fact, that which is indisputably the case. If a person remains unconvinced, they just need more convincing, not criticism.

Barbarian observes:
A bit of dark pigment allows a cell to become more sensitive to light.

Darwin said "How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated". He didn't seem to think how a cell senses light would be an issue. I disagree with him. We know a lot more about how it senses light and frankly, his theory and PE are floundering to explain such things.

No sarcasm intended but telling me a dark pigment allows a cell to sense light is similar to saying pushing a button on a radio allows a station to be received.

The difference, of course, is that in the case of the dark spot, the spot is the directly receptor, and of course, in the radio, the button is not. As you see, those highly-evolved molecules don't even exist in many organisms that can detect light and make use of that perception.

I only mentioned a radio to illustrate the need to be more technical if you want to explain where the "spot" came from or how a cell figured out how to use it.
Also, I don't know what you mean by a "highly-evolved" molecule. A molecule is the smallest part that reacts chemically. Even green algae use the all-trans-retina molecule to sense light. Molecular evolution isn't about the evolution of a molecule, it's about whether evolution took place within the cell on a molecular level.

In order to discuss the origin of a light sensitive cell we need to break it down more.

So tell me about light-detecting bacteria. How does that work, without the highly-evolved molecules you think are essential to vision?

Bacteria can't sense light without binding 13-cis-retinal to make Bacteriorhodopsin, halorhodopsin or proteorhodopsin. They convert a reaction to light to operate proton pumps, ion channels, and even g protein coupled receptors similar to the ones in eukaryotes.

An organ can be broken down to tissue, tissue broken down to cells. What allows a cell to sense light is a receptor in the cell membrane called an opsin.

What about bacteria that lack them, but still react usefully to light? They don't have opsins, but they have very primitive molecules called "rhodopsins" that work well enough. The protists, like Euglena, have pigments that are transitional between the very simple bacterial forms, and the complex forms in vertebrates.

Rhodopsin is a type of opsin. There is nothing "primitive" about a molecule. Chemical reactions don't change over time. I'm not sure why one would add words like "primitive" or "highly evolved" to describe a molecule. I'll guess that was just an exaggeration. There are large or small molecules but if a molecule changed it would be a compound or back to elements.

The simplest known photopigment is melatonin, sensitive because its darker

Melatonin is a hormone, so I'll assume you meant melanopsin.

See the research above. A simple dark receptor can detect light by absorbing it, transforming it to thermal energy, which the organism can then respond usefully. This is the simplest form of vision.

The research article was hypothesizing an evolutionary link between melatonin receptors and rhodopsin receptors. Melatonin is a hormone, melanopsin is the photopigment. Melanopsin does not transform light into thermal energy which a cell can usefully respond. Melanopsin binds to 11-cis-retinal to trigger a cascade.

Of course they don't use TRPV3, but they do have opsins.

Nope. They use a much simpler system, rhodopsins. And protists use some thing transitional between rhodopsins and opsins.

Rhodopsin is a type of opsin. I have no idea what you mean by something transitional between them. Nothing personal but I get the feeling you're making this stuff up. Can you explain that?

Since there is no evidence eukaryotic opsins evolved from prokaryotic opsins I fail to see the relavence.

Light-Sensing Protein Illuminates Sun-Loving Ocean Bacteria
PLoS Biol. 2005 August; 3(8): e287.
The presence of rhodopsin-like proteins in a wide range of life may eventually provide hints to the protein's evolutionary age. That this large class of transmembrane proteins was so well-conserved over a long evolutionary time scale provides evidence for complex ancient proteins. Another question that remains is whether the proteorhodopsin has any sensory function as does rhodopsin in humans, or whether the bacteria use the protein purely for energy transduction. ?
So, as you see, the evidence indicates that the evolutionary ancestors of opsins were used as photosynthetic molecules, and only later evolved as light sensors. Obviously, it isn't much of a jump from a molecule that can absorb and use light to make a chemical reaction go, to a molecule that can use light to make chemical reaction stimulate a neuron.

I don't see any of that from that article. They seemed to cite a few general facts and pose a lot of questions. There is no such thing as an "evolutionary ancestor of opsins", were talking about proteins not an organism. Saying "obviously, it isn't much of a jump..." just glosses over every problem ever raised for molecular evolution. It's like saying there isn't much of a jump from this:
CAA GAT GCC ATT GTC CCC CGG CCT CCT GCT GCT GCT GCT CTC CGG GGC CAC GGC

To this:
AGC ATA TGC AGG AAG CGG CAG GAA TAA GGA AAA GCA GCC TCC TGA CTT TCC TCG

I hate to point this out but that dark "substance" has been the topic of my posts. 11-cis is a chromophore(pigment).

Turns out, the precursors to this are much, much simpler.

The precursor to 11-cis-retinal is Vitamin A. Chemically similar, the difference is in shape, so not that much simpler.

 

[Barbarian]

Barbarian observes:
No one logically proved anything in science.

Good evening Barbarian! I have to say I don't think it's a good idea to grade all science on a curve, it only drags down the rest of science.

There's no "grading on a curve." It's just a limitation of the inductive method that science uses. It never gets logical certainty. That's true of all sciences, not just biology and physics.

Learn about it here:
Scientific theories are never proven completely. They are supported by facts, but they never become (ultimate, unchangeable) facts. As Carroll writes, we have to take “I believe x†to mean, not “I can prove x is the caseâ€, but “it would be unreasonable to doubt x.†The absence of a reasonable doubt (based on evidences) is what makes a scientific theory “trueâ€.
http://vishal12.wordpress.com/2009/0...oves-anything/

If you don't get this, you don't get science.

When someone puts it that way, it seems I have no choice but to agree with that. However, that last sentence is a subtle attack on truth.

No. It's just an admission that science cannot deal in absolute truth. You can never get that by looking at the evidence, because there's always the possibility that there is evidence you haven't yet seen.

In spite of that bullying tactic, I strongly disagree with that. If a theory were "true", it would be called a law or a fact.

No. Laws are weaker things than theories. Both laws and theories predict things, but theories also explain them, while laws cannot. Hence, Kepler's Law predicts how the planets will move around the Sun, while Newton's Theory of Gravitation explains why this happens, and thereby makes a much stronger statement, making it applicable not just to planets, but to every body in the universe. Theories are as strong as it gets in science. Unfortunately, the colloquial use of "theory" has confused many people.

The absence of a reasonable doubt is what makes a scientific theory convincing. What makes something in science true is when it acquires the status of a fact, that which is indisputably the case. If a person remains unconvinced, they just need more convincing, not criticism.

We do this by getting more evidence. As you know, the evidence for evolution has grown greatly since Darwin's time.

Barbarian observes:

A bit of dark pigment allows a cell to become more sensitive to light.
Darwin said "How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated". He didn't seem to think how a cell senses light would be an issue.

Turns out, it wasn't, compared to how life began. We now know a great deal about the evolution of vision, but we are just beginning to see how God brought life forth from the Earth.

I disagree with him. We know a lot more about how it senses light and frankly, his theory and PE are floundering to explain such things.

As you saw, Darwin's prediction that complex eyes were preceded by many small steps, has been confirmed by biologists. I showed you one set of steps on one phylum, but there are others. And molecular biologists have shown that the visual pigments were preceded by simpler substances that were also light-sensitive.

No sarcasm intended but telling me a dark pigment allows a cell to sense light is similar to saying pushing a button on a radio allows a station to be received.

The difference, of course, is that in the case of the dark spot, the spot is the direct receptor, and of course, in the radio, the button is not. As you see, those highly-evolved molecules don't even exist in many organisms that can detect light and make use of that perception.

I only mentioned a radio to illustrate the need to be more technical if you want to explain where the "spot" came from or how a cell figured out how to use it.

It wasn't a very good metaphor. You'd have to find a primitive device and compare it to a more advanced one of the same sort. A crystal radio, compared to a modern solid-state device.

Also, I don't know what you mean by a "highly-evolved" molecule.

One that has gone through many changes in evolution. Hall's bacteria, for example, started with a generalized protein and over time, it evolved into a very efficient enzyme, with a regulator protein. Highly evolved, because it went through many evolutionary changes.

A molecule is the smallest part that reacts chemically. Even green algae use the all-trans-retina molecule to sense light.

But simpler organisms do not. And we can see that these have evolved over time.

Molecular evolution isn't about the evolution of a molecule, it's about whether evolution took place within the cell on a molecular level.

Molecules can evolve, just like any other feature. Of course, evolution happens to populations, but the effect is quite visible in molecules.

In order to discuss the origin of a light sensitive cell we need to break it down more.

So tell me about light-detecting bacteria. How does that work, without the highly-evolved molecules you think are essential to vision?

Bacteria can't sense light without binding 13-cis-retinal to make Bacteriorhodopsin, halorhodopsin or proteorhodopsin. They convert a reaction to light to operate proton pumps, ion channels, and even g protein coupled receptors similar to the ones in eukaryotes.

Quite recently, they actually found a bacterium that was almost there:

A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties
February 25, 2011 The Journal of Biological Chemistry, 286, 5967-5976.
Abstract:
Rhodopsins possess retinal chromophore surrounded by seven transmembrane α-helices, are widespread in prokaryotes and in eukaryotes, and can be utilized as optogenetic tools. Although rhodopsins work as distinctly different photoreceptors in various organisms, they can be roughly divided according to their two basic functions, light-energy conversion and light-signal transduction. In microbes, light-driven proton transporters functioning as light-energy converters have been modified by evolution to produce sensory receptors that relay signals to transducer proteins to control motility. In this study, we cloned and characterized two newly identified microbial rhodopsins from Haloquadratum walsbyi. One of them has photochemical properties and a proton pumping activity similar to the well known proton pump bacteriorhodopsin (BR). The other, named middle rhodopsin (MR), is evolutionarily transitional between BR and the phototactic sensory rhodopsin II (SRII), having an SRII-like absorption maximum, a BR-like photocycle, and a unique retinal composition. The wild-type MR does not have a light-induced proton pumping activity. On the other hand, a mutant MR with two key hydrogen-bonding residues located at the interaction surface with the transducer protein HtrII shows robust phototaxis responses similar to SRII, indicating that MR is potentially capable of the signaling. These results demonstrate that color tuning and insertion of the critical threonine residue occurred early in the evolution of sensory rhodopsins. MR may be a missing link in the evolution from type 1 rhodopsins (microorganisms) to type 2 rhodopsins (animals), because it is the first microbial rhodopsin known to have 11-cis-retinal similar to type 2 rhodopsins.

But not quite. Still, it's another demonstration that the eukaryote system is evolved from simpler forms in prokaryotes.

An organ can be broken down to tissue, tissue broken down to cells. What allows a cell to sense light is a receptor in the cell membrane called an opsin.
What about bacteria that lack them, but still react usefully to light? They don't have opsins, but they have very primitive molecules called "rhodopsins" that work well enough. The protists, like Euglena, have pigments that are transitional between the very simple bacterial forms, and the complex forms in vertebrates.

Rhodopsin is a type of opsin.

It's just less evolved. As you see, a very primitive form has recently been found in ocean bacteria.

There is nothing "primitive" about a molecule. Chemical reactions don't change over time.

Hall's bacteria were directly observed to have their chemical reactions change over time.

I'm not sure why one would add words like "primitive" or "highly evolved" to describe a molecule.

Because (like the one Hall saw evolve) they change over time.

I'll guess that was just an exaggeration.

Directly observed to happen.

There are large or small molecules but if a molecule changed it would be a compound

All molecules are compounds unless they are composed of all the same kind of atom.

See the research above. A simple dark receptor can detect light by absorbing it, transforming it to thermal energy, which the organism can then respond usefully. This is the simplest form of vision.

The research article was hypothesizing an evolutionary link between melatonin receptors and rhodopsin receptors. Melatonin is a hormone, melanopsin is the photopigment. Melanopsin does not transform light into thermal energy which a cell can usefully respond. Melanopsin binds to 11-cis-retinal to trigger a cascade.

But it does. Any darker pigment does that. And, as you read, the evidence shows evolution of the pigment from simpler forms in invertebrates. And a form of melanopsin has now been found in invertebrates.

They use a much simpler system, rhodopsins. And protists use some thing transitional between rhodopsins and opsins.

Rhodopsin is a type of opsin.

It's quite different, a simpler form, which is somewhat less efficient.

I have no idea what you mean by something transitional between them. Nothing personal but I get the feeling you're making this stuff up. Can you explain that?

The Rhodopsins in protists are more like the opsins in vertebrates, than the more primitive rhodopsins in bacteria.

Light-Sensing Protein Illuminates Sun-Loving Ocean Bacteria
PLoS Biol. 2005 August; 3(8): e287.
The presence of rhodopsin-like proteins in a wide range of life may eventually provide hints to the protein's evolutionary age. That this large class of transmembrane proteins was so well-conserved over a long evolutionary time scale provides evidence for complex ancient proteins. Another question that remains is whether the proteorhodopsin has any sensory function as does rhodopsin in humans, or whether the bacteria use the protein purely for energy transduction. ?

So, as you see, the evidence indicates that the evolutionary ancestors of opsins were used as photosynthetic molecules, and only later evolved as light sensors. Obviously, it isn't much of a jump from a molecule that can absorb and use light to make a chemical reaction go, to a molecule that can use light to make chemical reaction stimulate a neuron.

I don't see any of that from that article.

They note that this particular rhodopsin is used to generate energy. It indicates that the energy function came first, and sensory only later. There is evidence that proteorhodopsin has primitive sensory functions:

Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea" Science 289 (5486): 1902–1904.

They seemed to cite a few general facts and pose a lot of questions. There is no such thing as an "evolutionary ancestor of opsins", were talking about proteins not an organism.

It's impossible to deny what's there.

Saying "obviously, it isn't much of a jump..." just glosses over every problem ever raised for molecular evolution.

See above. Turns out it has evolved to a sensory function.

It's like saying there isn't much of a jump from this:
CAA GAT GCC ATT GTC CCC CGG CCT CCT GCT GCT GCT GCT CTC CGG GGC CAC GGC

To this:
AGC ATA TGC AGG AAG CGG CAG GAA TAA GGA AAA GCA GCC TCC TGA CTT TCC TCG

Mendel discovered that fact, a long time ago.

 

[Vaccine]

"Model of the energy generating mechanism in marine bacteria. When sunlight strikes a rhodopsin molecule (1), it changes its configuration such that a proton is expelled from the cell (2). The chemical potential causes the proton to flow back into the cell (3), thus generating energy (4) in the form of adenosine triphosphate (5)."

This is a surprisingly simple and primitive phosphorylation mechanism, (phosphorylation is the basis of energy production in all cells).

Good morning Barbarian! It may seem simple compared to system in a mammal, but the question remains how did/could that system evolve? Even in that simple mechanism there are 5 steps. Remove one of those steps and the system will not function. What good is an valve(1) without a pump (3)? What good is a pump(3) without the valve(1)? Minor detail, but they didn't mention there are also gates for the ion channel(valve) to prevent backward flow and other proteins to convert rhodopsin(pump) back for the next cycle (depending on the organism happens 100-1000 times per second).
Even with a single cascade like that there is irreducible complexity. Looking at the ion channel(1), which functions as a valve, it has a specific structure to allow it to bind to the membrane and a gate to filter unwanted particles out and only allow specific ones in. Without a pump to change the potential, this feature would be useless. Looking at rhodopsin(3), which acts as a pump, it needs a specific chromophore to react to light, and specific proteins that return it to its original shapr for the next cycle. Without a valve to regulate the potential, the pump would suck the cell empty. There are no functional precursors of an ion channel or rhodopsin to select. Since there is nothing to select, natural selection fails to explain this system.
'If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.' -Darwin

I agree with Darwin. So how do we explain this?

"ID holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection"
http://www.intelligentdesign.org/

 

[Asyncritus]

I'm afraid you misunderstand, barbarian.

It is 'sight' itself that evolution os being called uopn to account for.

You open your eyes, and you 'see'.

We don't want the physicochemical and mechanical bits you can dredge up from somewhere. It's sight itself that's your problem.

How does anything see? And how does it know what it's 'seeing'?

That's your real problem, and it won't go away.

 

[Barbarian]

I'm afraid you misunderstand, barbarian.
It is 'sight' itself that evolution os being called uopn to account for.
You open your eyes, and you 'see'.

So your argument is that only complex vertebrate eyes, with eyelids can have "sight?" What about all those other, simpler eyes? Don't they see?

We don't want the physicochemical and mechanical bits you can dredge up from somewhere. It's sight itself

Sight is based on those processes and substances. So if you want to understand how sight came to be, you have to know about the way it actually works.

that's your problem.

The evidence shows that it evolved. So no problem for science. As in all sciences, there are still many things for us to yet discover. But the evolution of vision is very well-established.

How does anything see?

Light-sensitive substances can transform electromagnetic energy into chemical energy, which makes neurons fire.

And how does it know what it's 'seeing'?

I don't think a scallop "knows" anything. But it can see a predator and take action accordingly.

That's your real problem,

As you see, it's not a problem for science; the way that complex eyes evolved is quite clear.

 

[Vaccine]

No. Laws are weaker things than theories.

I disagree. A law holds that something happens without exception. A scientic theory is a work in progress, working to become a law. Also, contrary to wiki a law does have explaining power. Since it is something that happens without exception, there is nothing to predict.

And molecular biologists have shown that the visual pigments were preceded by simpler substances that were also light-sensitive.

That is simply not true. There are no more black boxes to invoke. There are no precursors to light sensitive molecules, they are the smallest, simplest compounds that can react to light.

I only mentioned a radio to illustrate the need to be more technical if you want to explain where the "spot" came from or how a cell figured out how to use it.

It wasn't a very good metaphor. You'd have to find a primitive device and compare it to a more advanced one of the same sort. A crystal radio, compared to a modern solid-state device.

If we aren't going to be technical I could say how a cell works is similar to a circuit board. The protein components like 11-cis-retinal, rhodopsin, transducin, GTP are similar to transistors, resistors, capacitors, semiconductors and microchips. Depending on the function, those components are aligned in a circuit to accomplish a certain task.

Hall's bacteria, for example, started with a generalized protein and over time, it evolved into a very efficient enzyme, with a regulator protein. Highly evolved, because it went through many evolutionary changes.

Hall's bacteria were directly observed to have their chemical reactions change over time.

Don't take this personal, I know you've taught me a thing or two, but in this case I don't think you fully comprehend Hall's argument.
Chemical reactions are fixed. Enzymes are made from proteins, they didn't evolve. Even if we think of evolve as synoymous with change over time, it's still reaching. It's like saying salt evolved to saltwater.
Hall's argument was he removed part of the path for the bacteria to make the enzyme, it found a new way to make it, so it's not irreducibly complex but evolution in action. The answer to his argument is it was making the same enzyme, just in a different way. There other path was already there so nothing evolved, there is redundancy built into the genome. Like the circuitboard analogy, it is possible to build a circuit with redundant paths and error protection. I admit that isn't a very technical explanation and don't expect it to be taken seriously. I just wanted to show the need for a more technical explanation. So I'm not making a double standard, if I have time later I will go into more technical detail about just exactly how those paths were already there.

Molecules can evolve, just like any other feature. Of course, evolution happens to populations, but the effect is quite visible in molecules.

I'm still not sure what you mean. Molecules can be simple like water or extremely complex like ATP synthase, depending on their atomic size and structure. They can have different forms and functions, but I don't get using the term evolve to describe chemical reactions.
http://www.arn.org/docs/mm/atpmechanism.htm

Quite recently, they actually found a bacterium that was almost there:

A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties
February 25, 2011 The Journal of Biological Chemistry, 286, 5967-5976.
Abstract:
Rhodopsins......................One of them has photochemical properties and a proton pumping activity similar to the well known proton pump bacteriorhodopsin (BR). The other, named middle rhodopsin (MR), is evolutionarily transitional between BR and the phototactic sensory rhodopsin II (SRII), having an SRII-like absorption maximum, a BR-like photocycle, and a unique retinal composition. The wild-type MR does not have a light-induced proton pumping activity. On the other hand, a mutant MR with two key hydrogen-bonding residues located at the interaction surface with the transducer protein HtrII shows robust phototaxis responses similar to SRII, indicating that MR is potentially capable of the signaling. These results demonstrate that color tuning and insertion of the critical threonine residue occurred early in the evolution of sensory rhodopsins. MR may be a missing link in the evolution from type 1 rhodopsins (microorganisms) to type 2 rhodopsins (animals), because it is the first microbial rhodopsin known to have 11-cis-retinal similar to type 2 rhodopsins.

But not quite. Still, it's another demonstration that the eukaryote system is evolved from simpler forms in prokaryotes.

It does not demonstrate that at all. It demonstrated critical parts and photoreceptive properties of 11-cis-retinal were present in a rhodopsin of a microbe. Even though they're isotopes 11-cis-retinal works better than 13-cis-retinal. It didn't work as a pump or signal, so that's kinda a big deal. It is unique and interesting, but not conclusive.

Rhodopsin is a type of opsin.

It's just less evolved. As you see, a very primitive form has recently been found in ocean bacteria.

Rhodopsin is a type of opsin.

It's quite different, a simpler form, which is somewhat less efficient.

Rhodopsin is a type of opsin

They use a much simpler system, rhodopsins. And protists use some thing transitional between rhodopsins and opsins.

Can you explain that?

The Rhodopsins in protists are more like the opsins in vertebrates, than the more primitive rhodopsins in bacteria.

Light-Sensing Protein Illuminates Sun-Loving Ocean Bacteria
PLoS Biol. 2005 August; 3(8): e287.
The presence of rhodopsin-like proteins in a wide range of life may eventually provide hints to the protein's evolutionary age. That this large class of transmembrane proteins was so well-conserved over a long evolutionary time scale provides evidence for complex ancient proteins. Another question that remains is whether the proteorhodopsin has any sensory function as does rhodopsin in humans, or whether the bacteria use the protein purely for energy transduction. ?

So, as you see, the evidence indicates that the evolutionary ancestors of opsins were used as photosynthetic molecules, and only later evolved as light sensors. Obviously, it isn't much of a jump from a molecule that can absorb and use light to make a chemical reaction go, to a molecule that can use light to make chemical reaction stimulate a neuron.

I think I see where the problem is, "The Rhodopsins in protists are more like the opsins in vertebrates". They mean opsin as in type, family, group.
Opsin- (biochemistry) - Any of several compounds that form the protein component of the light-sensitive retina pigment, rhodopsin

http://dictionary.reference.com/browse/opsin

And yes, it is a huge jump from a light pump to a light sensor.

They note that this particular rhodopsin is used to generate energy. It indicates that the energy function came first, and sensory only later..... Turns out it has evolved to a sensory function.

Thats a huge jump. Can you explain it in more detail?

 

[Barbarian]

Barbarian observes:
No. Laws are weaker things than theories.

I disagree. A law holds that something happens without exception.

No, the 2nd Law of Thermodynamics, for example, says that entropy will never decrease. With the exception of open systems, where entropy can decrease so long as energy is being added from outside.

A scientic theory is a work in progress, working to become a law.

No. As you learned, Laws merely predict. Theories predict and explain. Hence Newton's Theory of Gravitation is more powerful and useful than Kepler's Laws. Each is about the same thing, but Newton's is a theory, and therefore more certain than Kepler's.

Also, contrary to wiki a law does have explaining power.

No. For example, the 2nd Law of Thermodynamics does not explain why heat only moves from hotter things to colder things. But kinetic theory does explain this, and it is a more useful thing than the 2nd Law.
http://en.wikipedia.org/wiki/History_of_thermodynamics

Since it is something that happens without exception, there is nothing to predict.

Understanding why planets move as they do, is critical for all engineering problems that touch on gravity. Understanding why heat only travels from hot to cold, is critical for many, many applications in physics.

Barbarian observes:
And molecular biologists have shown that the visual pigments were preceded by simpler substances that were also light-sensitive.

That is simply not true.

Demonstrably so. For example, the most primitive rhodopsin known, turns out to be a means for bacteria to do phosphorylation (critical to all cells for energy).

There are no more black boxes to invoke. There are no precursors to light sensitive molecules, they are the smallest, simplest compounds that can react to light.

Nope.
Some microorganisms contain proteins that can interact with light and convert it into energy for growth and survival, or into sensory information that guides cells towards or away from light. The simplest energy-harvesting photoproteins are the rhodopsins, which consist of a single, membrane-embedded protein covalently bound to the chromophore retinal (a light-sensitive pigment) [1]. One class of archaeal photoproteins (called bacteriorhodopsin) was shown to function as a light-driven proton pump, generating biochemical energy from light [2],[3].
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000359

The simplest light-sensitive substance, BTW, is silver nitrate. The simplest organic substance that is sensitive to light... (Barbarian checks)

Indole-3-acetic acid

It's an auxin, a substance sensitive to light, that is responsible for plants growing toward the Sun.

Pretty simple, no?

I only mentioned a radio to illustrate the need to be more technical if you want to explain where the "spot" came from or how a cell figured out how to use it.

It wasn't a very good metaphor. You'd have to find a primitive device and compare it to a more advanced one of the same sort. A crystal radio, compared to a modern solid-state device.

Barbarian observes:
Hall's bacteria, for example, started with a generalized protein and over time, it evolved into a very efficient enzyme, with a regulator protein. Highly evolved, because it went through many evolutionary changes.

Hall's bacteria were directly observed to have their chemical reactions change over time.

Don't take this personal, I know you've taught me a thing or two, but in this case I don't think you fully comprehend Hall's argument.

I hope I do. I've taught classes about it.

Chemical reactions are fixed. Enzymes are made from proteins, they didn't evolve.

This one was observed to evolve over time. The final version was considerably more effective than the generalized form that the bacteria changed over a series of mutations via natural selection.

Even if we think of evolve as synoymous with change over time, it's still reaching. It's like saying salt evolved to saltwater.

No. It's still salt, same chemical composition. This enzyme changes in amino acid sequence over time, altering its shape, which of course altered it's efficiency as an enzyme.

Hall's argument was he removed part of the path for the bacteria to make the enzyme, it found a new way to make it, so it's not irreducibly complex but evolution in action.

By Behe's definition, it's irreducibly complex:
A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. (Darwin's Black Box p39 in the 2006 edition)

The final system is composed of the enzyme, the substrate it metabolizes, and a regulator (which is activated only in the presence of the substrate, which means the enzyme will not be produced unless there is the substrate in the environment.

So, we have three interacting components, and the removal of any one of them from the system causes the system to cease functioning.

The answer to his argument is it was making the same enzyme, just in a different way.

Nope. Different enzyme that does the same thing. And it evolved gradually, in a series of steps. It is not the same enzyme.

There other path was already there

Nope. The new enzyme is not the same as the old one. You see, the only part that matters in an enzyme is the shape of the active site. The rest of it can be made of entirely different sequences of amino acids so long as they don't interfer with the active site. And there are normally several ways the active site can be constructed, each of them using different sequences.

So that excuse won't work here.

Barbarian observes:
Molecules can evolve, just like any other feature. Of course, evolution happens to populations, but the effect is quite visible in molecules.

I'm still not sure what you mean.

As in the case you just read, a molecule that was effectively inactive with the specific substrate, evolved gradually in a series of steps to become very efficient. Each of the steps was somewhat better than the one before; not by design; it's just that mutations that made it somewhat better were preserved, and the many other mutations that did not make it better were discarded by natural selection.

Molecules can be simple like water or extremely complex like ATP synthase, depending on their atomic size and structure. They can have different forms and functions, but I don't get using the term evolve to describe chemical reactions.

The shape of the enzyme gradually changed. Here's how it works:

1. A molecule is effectively inactive with a specific substrate.
2. A random mutation, affecting the amino acid sequence changes the shape of the molecule, making it more effective at catalyzing the reaction.
3. Other mutations that don't make it so effective are lost, as the bacteria having them are unable to compete with the more effective ones.
4. This more effective group form the new gene pool, and the process repeats.
5. Eventually, the molecule evolves into a very efficient form.

Quote Originally Posted by Barbarian View Post
Quite recently, they actually found a bacterium that was almost there:

A Microbial Rhodopsin with a Unique Retinal Composition Shows Both Sensory Rhodopsin II and Bacteriorhodopsin-like Properties
February 25, 2011 The Journal of Biological Chemistry, 286, 5967-5976.
Abstract:
Rhodopsins......................One of them has photochemical properties and a proton pumping activity similar to the well known proton pump bacteriorhodopsin (BR). The other, named middle rhodopsin (MR), is evolutionarily transitional between BR and the phototactic sensory rhodopsin II (SRII), having an SRII-like absorption maximum, a BR-like photocycle, and a unique retinal composition. The wild-type MR does not have a light-induced proton pumping activity. On the other hand, a mutant MR with two key hydrogen-bonding residues located at the interaction surface with the transducer protein HtrII shows robust phototaxis responses similar to SRII, indicating that MR is potentially capable of the signaling. These results demonstrate that color tuning and insertion of the critical threonine residue occurred early in the evolution of sensory rhodopsins. MR may be a missing link in the evolution from type 1 rhodopsins (microorganisms) to type 2 rhodopsins (animals), because it is the first microbial rhodopsin known to have 11-cis-retinal similar to type 2 rhodopsins.

But not quite. Still, it's another demonstration that the eukaryote system is evolved from simpler forms in prokaryotes.

It does not demonstrate that at all.

Yes it does. It demonstrated critical parts and photoreceptive properties of 11-cis-retinal were present in a rhodopsin of a microbe. Even though they're isotopes 11-cis-retinal works better than 13-cis-retinal.

I think you mean "isomer." "Isotopes" are elements with differing numbers of neutrons. But they aren't isomers, since they don't have the same chemical formula.

It didn't work as a pump or signal, so that's kinda a big deal. It is unique and interesting, but not conclusive.

Just another bit of evidence on the mountain of evidence.

Rhodopsin is a type of opsin.

It's just less evolved. As you see, a very primitive form has recently been found in ocean bacteria.

Rhodopsin is a type of opsin.

It's quite different, a simpler form, which is somewhat less efficient.

Rhodopsin is a type of opsin

Barbarian observes:
They use a much simpler system, rhodopsins. And protists use some thing transitional between rhodopsins and opsins.

Can you explain that?

The Rhodopsins in protists are more like the opsins in vertebrates, than the more primitive rhodopsins in bacteria.

Light-Sensing Protein Illuminates Sun-Loving Ocean Bacteria
PLoS Biol. 2005 August; 3(8): e287.
The presence of rhodopsin-like proteins in a wide range of life may eventually provide hints to the protein's evolutionary age. That this large class of transmembrane proteins was so well-conserved over a long evolutionary time scale provides evidence for complex ancient proteins. Another question that remains is whether the proteorhodopsin has any sensory function as does rhodopsin in humans, or whether the bacteria use the protein purely for energy transduction.

So, as you see, the evidence indicates that the evolutionary ancestors of opsins were used as photosynthetic molecules, and only later evolved as light sensors. Obviously, it isn't much of a jump from a molecule that can absorb and use light to make a chemical reaction go, to a molecule that can use light to make chemical reaction stimulate a neuron.

I think I see where the problem is, "The Rhodopsins in protists are more like the opsins in vertebrates". They mean opsin as in type, family, group.
Opsin- (biochemistry) - Any of several compounds that form the protein component of the light-sensitive retina pigment, rhodopsin

Learn about it here:
http://en.wikipedia.org/wiki/Opsin

and here:
http://en.wikipedia.org/wiki/Bacterial_rhodopsins

Notice that the simplest of these are merely proton-tranfer agents, for phosphorylation, not sensory at all.

And yes, it is a huge jump from a light pump to a light sensor.

Not a light pump. An energy pump. And as you see, one of the most primitive of the rhodopsins, proteorhodopsin can do both.

So obviously not a big jump from one to the other.

Barbarian observes:
They note that this particular rhodopsin is used to generate energy. It indicates that the energy function came first, and sensory only later..... Turns out it has evolved to a sensory function.

Thats a huge jump.

Since both functions work in the same molecule, it wouldn't seem so.

Can you explain it in more detail?

The same light-sensitivity that allows it to produce ATP, allows it to stimulate the cell, or a neuron.

Remember, all cell interactions are really energy exchanges.

 

[Sparkey]

Pardon my interjection regarding Laws. Newton's law of universal gravitation states that every point mass in the universe attracts every other point mass with a force that is directly proportional to the product of their masses and inversely proportional to the square of the distance between them. So in that sense it does 'explain' things. It does not go on to try to say why but leaves off as a generalization of observed facts that are known true (at that time) without exception. Newton and others found this law useful to predict the behavior of a dropped object, for instance, but it didn't attempt to explain why gravitation happened.

My thoughts on "proof" include the implication that it can never be wrong (take the Word of God, for instance) but that is altogether different from what is meant by scientists when they use the term. It's off-topic but I hope that this helps.

 

[Barbarian]

Precisely so. Newton explained the motion of planets (and the falling of apples, and a lot of other things) by hypothesizing a force that was proportional to the masses of two things, but inversely proportional to the square of the distance between them. Experimentation has shown that he was right to a very high level of precision. The "error" had mostly to do with very large masses and very high velocities, in which relativity becomes significant.

 

[Vaccine]

Barbarian observes:
No. Laws are weaker things than theories.

Ok, we are just going to have to agree to disagree there.

Barbarian observes:
And molecular biologists have shown that the visual pigments were preceded by simpler substances that were also light-sensitive.

That is simply not true.

Demonstrably so. For example, the most primitive rhodopsin known, turns out to be a means for bacteria to do phosphorylation (critical to all cells for energy).

The observation is just not true, Barbarian. ALL visual pigments consist of an opsin combined with the chromophore 11-cis-retinal. Since they all use 11-cis-retianal, there are no predecessors. Other rhodopsins use isomers of retinal, but there is no "simpler substance" relevant to visual pigments.

Also, the bacteria rhodopsin is not a visual pigment, it uses an isomer of 11-cis-retinal, and there is no relation between eukaryote rhodopsins and prokaryote rhodopsins.

"In the past few years, genetic tools have revealed several parallel pathways through which light guides behavior and have provided insights into the convergent evolution of eyes."
http://www.sciencemag.org/content/313/5795/1914.abstract?sid=82caf2d3-d85d-4694-9859-ef125b752822

The simplest light-sensitive substance, BTW, is silver nitrate. The simplest organic substance that is sensitive to light... (Barbarian checks)

Indole-3-acetic acid

It's an auxin, a substance sensitive to light, that is responsible for plants growing toward the Sun.

Pretty simple, no?

Yes, nice to know that's the simplest. Not that it matters but it's an inorganic compound.

Molecules can be simple like water or extremely complex like ATP synthase, depending on their atomic size and structure. They can have different forms and functions, but I don't get using the term evolve to describe chemical reactions.

The shape of the enzyme gradually changed. Here's how it works:

A molecule is effectively inactive with a specific substrate.
A random mutation, affecting the amino acid sequence changes the shape of the molecule, making it more effective at catalyzing the reaction.
Other mutations that don't make it so effective are lost, as the bacteria having them are unable to compete with the more effective ones.
This more effective group form the new gene pool, and the process repeats.
Eventually, the molecule evolves into a very efficient form.

My comment was about using the term evolve to describe chemical reactions. I can't make any sense from that reply, it begins with a molecule then switches to mutated gene sequence. Evolution applies to species, not chemical reactions.

It demonstrated critical parts and photoreceptive properties of 11-cis-retinal were present in a rhodopsin of a microbe. Even though they're isotopes 11-cis-retinal works better than 13-cis-retinal.

I think you mean "isomer." "Isotopes" are elements with differing numbers of neutrons. But they aren't isomers, since they don't have the same chemical formula.

You're right, I meant isomers not isotope. They are isomers.

And yes, it is a huge jump from a light pump to a light sensor.

Not a light pump. An energy pump. And as you see, one of the most primitive of the rhodopsins, proteorhodopsin can do both.

I meant light-driven pump. Proteorhodopsin doesn't do both. Even if it did, both systems are irreducibly complex. There are several changes that would have to be made at the same time to change a pump into a sensor.

 

[Vaccine]

Here is a better, more detailed, reply of how Kenneth Miller's claims are false.
According to Miller, Hall's experiment from 1970 was to:
“[use] the tools of molecular genetics to wipe out an existing multipart system and then see if evolution can come to the rescue with a system to replace it.” (Miller 1999, 145)

In Hall's experiment from the 1970's he deleted a gene for just the ß-galactosidase of the lac operation.

"All of the other functions for lactose metabolism, including lactose permease and the pathways for metabolism of glucose and galactose, the products of lactose hydrolysis, remain intact, thus re-acquisition of lactose utilization requires only the evolution of a new ß-galactosidase function." (Hall 1999)

Miller's clam of a multi-part system being wiped out isn't true. Only a single gene was wiped out. Not only that but that gene he wiped out functioned as part of the on/off switch for the system, the rest remained intact.

According to Hall:
"Professor Hall pointed out that both the lac and ebg ß-galactosidase enzymes are part of a family of highly-conserved ß-galactosidases, identical at 13 of 15 active site amino acid residues, which apparently diverged by gene duplication more than two billion years ago."

Again Miller was mistaken, evolution did not come up with a system to replace it, a near identical pre-existing gene was already there before the experiment even began. Further, even though ebg ß-galactosidase served another function there was overlap because it worked at 10% efficiency of ß-galactosidase. The system and enzyme function were pre-existing.

According to Hall:
"The mutations described above have been deliberately selected in the laboratory as a model for the way biochemical pathways might evolve so that they are appropriately organized with respect to both the cell and its environment. It is reasonable to ask whether this model might have any relationship to the real world outside the laboratory. If it is assumed that the selection is strictly for lactose utilization, then a growth advantage exists only when all three mutations are present simultaneously. (Hall 1982a)"

No natural selection whatsoever. There were three steps to get from the deleted gene, to a functional one and the scientists choose every step. It wasn't just a case of speeding up natural selection, Miller didn't address this minor detail.

"Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)"
IPTG is an agent which stimulates ß-galactosidase production. In other words if they didn't add the stimulant, all the bacteria died. They kept the e.coli alive with a stimulant and choose every step. In their defense, they acknowledged there wasn't any relation to the real world.
So Miller ether grossly misrepresented the facts or just didn't understand what the experiment was about.
Here is a summary by Behe:
"He showed that the activity of a deleted enzyme could be replaced only by mutations to a second, homologous protein with a nearly-identical active site; and only if the second repressor already bound lactose; and only if the system were also artificially supported by inclusion of IPTG; and only if the system were also allowed to use a preexisting permease. Such results are exactly what one expects of irreducible complexity requiring intelligent intervention, and of limited capabilities for Darwinian processes."

Barbarian observes:
Hall's bacteria, for example, started with a generalized protein and over time, it evolved into a very efficient enzyme, with a regulator protein. Highly evolved, because it went through many evolutionary changes.

I can't make any sense of that. Generalized protein? Highly evolved because it evolved?

 

[Barbarian]

Here is a better, more detailed, reply of how Kenneth Miller's claims are false.

I don't think you're going to like the way this turns out...

According to Miller, Hall's experiment from 1970 was to:
“[use] the tools of molecular genetics to wipe out an existing multipart system and then see if evolution can come to the rescue with a system to replace it.†(Miller 1999, 145)

In Hall's experiment from the 1970's he deleted a gene for just the ß-galactosidase of the lac operation.

"All of the other functions for lactose metabolism, including lactose permease and the pathways for metabolism of glucose and galactose, the products of lactose hydrolysis, remain intact, thus re-acquisition of lactose utilization requires only the evolution of a new ß-galactosidase function." (Hall 1999)

Miller's clam of a multi-part system being wiped out isn't true. Only a single gene was wiped out. Not only that but that gene he wiped out functioned as part of the on/off switch for the system, the rest remained intact.

Miller uses Behe's own ideas on him:
Behe says that Hall did not wipe out a "multipart system" as I claimed; he deleted just one gene. Well, that's what I wrote, too. My description clearly and correctly states that Hall started his experiments "by deleting the structural gene for galactosidase," a single gene. However, I did indeed write that this deletion had knocked out a "multipart system." Why? Because once the gene was deleted, three components had to evolve to replace its function: First, a new galactosidase enzyme, second, a new lactose-sensitive control region, and third, a new way to switch on the lac permease gene. And, just as Futuyma and I pointed out, that's exactly what happened - all three parts eventually evolved.
http://www.millerandlevine.com/km/evol/DI/AcidTest.html

Behe was being disingenuous by redefining what he meant by a multipart system being knocked out.

Again Miller was mistaken, evolution did not come up with a system to replace it, a near identical pre-existing gene was already there before the experiment even began.

And here Behe is not being honest; he's quite aware that evolution never makes anything de novo, but always modifies something already there. Which is exactly what happened here. A protein that had very low specificity evolved over time to become very efficient for this particular substrate. Again, remember; evolution never makes anything from scratch; it merely modifies something already there.

No natural selection whatsoever.

Hall documented that there was. In fact, he was surprised to find a regulator had evolved at the end. That was something he had not anticipated.

There were three steps to get from the deleted gene, to a functional one and the scientists choose every step.

Wrong again. Hall says random mutations, and he didn't pick any of them.

"Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)"
IPTG is an agent which stimulates ß-galactosidase production. In other words if they didn't add the stimulant, all the bacteria died. They kept the e.coli alive with a stimulant and choose every step. In their defense, they acknowledged there wasn't any relation to the real world.

So in this particular environment, natural selection produced a new, irreducibly complex enzyme system. By Behe's own definition.

In other environments, it would have done something different. The IPTG issue is just a bunny trail to cover what Hall discovered.

Behe writes:

He showed that the activity of a deleted enzyme could be replaced only by mutations to a second, homologous protein with a nearly-identical active site;

No. Hall found no such limitation. Natural selection just picked the best protein to modify. In doing so, it evolved to become very efficient, albeit not in the same way as the enzyme that was originally knocked out.

and only if the second repressor already bound lactose; and only if the system were also artificially supported by inclusion of IPTG; and only if the system were also allowed to use a preexisting permease.

In other words, the organism had a multipart system knocked out by the deletion of an enzyme (Behe's definition). Then, a new enzyme evolved to take the place of it, by natural selection (no one picked which mutations would happen; a large number of them did happen, but only the advantageous ones were preserved). Then, unexpectedly, a regulator evolved. The resulting new system consisted of a newly-evolved enzyme, a newly-evolved regulator, and the material on which it would act. Because of the regulator, all three must be present in order for the new system to work. Which is Behe's definition of irreducible complexity.

Such results are exactly what one expects of irreducible complexity requiring intelligent intervention, and of limited capabilities for Darwinian processes."

I'm sure everyone would be interested in seeing Behe's evidence that Hall selected the mutations that happened, or that he intervened to preserve the ones that were preserved. Behe has been very reluctant to do that. I think I know why.