The eyeball as testimony to evolution?

Hi Patrick -

I appreciate your sincerity. Your command of the biology research literature probably needs a little reinforcement, however. Here is a popular article describing how biologists have discovered the mutation-by-mutation pathways to two different antifreeze genes in different fish species.

Best,
Chris

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What about the mutations that separate humans and chimps?

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That isn’t quite what I meant, but taking it as fact, doesn’t change the fish. The otothens are still otothens, and the Arctic Cod are still Arctic Cod.

One thing that tells me his bias is this:

They found a hit—but in a functionless stretch of cod DNA that doesn’t include any genes at all. Somehow, this region of useless junk gave rise to a new and very useful gene.

And then total fantasy.

First, through random chance, a short stretch of junk DNA was duplicated twice, creating four identical segments in a row. The stretches between these segments were very close to the code for the thralala unit, and through a single mutation, one of them turned into exactly the right code. This snippet then duplicated, over and over, creating the core of a new antifreeze gene.

And right into Lamarkian evolution. Why is not science. Why is religion, or philosophy.

We not only know that it evolved, but also why —to prevent the cod from icing over.

What about them? We aren’t related, just created similarly. Mutations will kill an animal long before creating any new kind.

Aren’t the genetic differences between chimps and humans responsible for the physical differences between the two species? Aren’t those differences useful for each species?

If changing a genome will kill an animal then how are humans and chimps able to survive when there are ~40 million changes between our genomes?

First, Do they have actual DNA from before and after this supposed mutation? From full humans, not supposed ancestors. Remember the Goddidit arguments also apply to mutationsdidit.

The Smithsonian mag seems to lead with the conclusion and base its findings on what they want to see. How can they prove which way the change went, from tolerant or intolerant?

Differences, not mutations.

We aren’t directly related. We have similarities and differences, not changes.

Actually, it appears to be a relatively complex story, but fascinating.

They are single base substitutions in an intron upstream of the human lactase gene. Are you saying substitution mutations don’t happen?

Let’s do a little math. Each human is born with 50 to 100 substitution mutations. These are mutations that change a single base. There are 6 billion bases in a diploid human genome, and 3 possible
substitution mutations at each position in that genome. That means there are 18 billion possible mutations. 18 billion divided by 50 mutations is 360 million which means you need about 360 million births to get every possible substitution mutation in the human genome. There are enough humans on the Earth to get every possible mutation 19 times over. Not all mutations have the same probability, bu this is a rough back-of-the-envelope calculation.

So can you explain why you think this is such an impossibility for a single substitution mutation to result in lactase persistance?

What’s the difference between them? If mutations created the same ~40 million differences between humans and chimps would it have a different outcome?

I’m saying it would be more in line with what we see in nature to lose an ability we once had, not gain a new one. If the difference involves a loss of information, it could go either way. Just claiming mutations for any differences is like saying God did it.

Genetic changes such as those that gave rise to the de novo antifreeze gene are the exact opposite of LaMarck. How you could confound the two is completely puzzling.

I get that you hate evolution, Patrick. But your lack of understanding about biology is hindering our ability to have a fruitful conversation. What can be done?

Best,
Chris

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I get that you are saying that, but I am not seeing you present any evidence to back it up.

The big difference is that we can observe mutations happening in the wild and in the lab. So no, they are not the same. We observe that humans are born with 50 to 100 substitution mutations. We observe mutations happening in bacterial populations in the lab. We see them happening all over the place. Where do we observe a deity directly changing DNA?

Also, we are not just claiming that mutations are responsible for the differences between species. We have evidence that mutations were the cause. Substitution mutations are biased towards transitions over transversions. A transition mutation is the substitution of a similar base:

image

A base with one ring is more likely to be substituted with the other base that has one ring, and the same for bases with two ring structures. When we look at the distribution of mutations that happen in real time (de novo mutations) we see that they match the variation in the human gene pool:

The pattern of differences that separate humans is the same pattern produced by the observed and natural processes that produce substitution mutations. So what if we compare the human and chimp genomes?

Again, the patterns match. The pattern of naturally occurring mutations matches the differences between the human and chimp genomes. You can find this evidence discussed here and also at this very website:

We don’t just assume that mutations are the cause of the differences. We have the evidence.

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What do I think of the articles? I read three of the cited articles. Their explanatory value for the origin of the eye was massively underwhelming. That is not surprising—that is the general nature of evolutionary explanations—minimal evidence, significantly overstated claims.

“Quite possibly, the human eye has originated from light-sensitive cells in the brain. Only later in evolution would such brain cells have relocated into an eye and gained the potential to confer vision.”

“Quite possibly?” Or not. How did these brain cells relocate into an eye? A miraculous eye is there, at the ready to accept the light sensitive cells and now provide a survival advantage to the organization. No explanation how that could have happened, no evidence that it ever did. But since evolution is “true” and eyes exist, PBTE (Praise Be To Evolution), evolution did it. “Evolution, help thou my unbelief.” In another post, creationists were mischaracterized as demanding a molecule by molecule explanation of how the eye evolved (a red herring even if true.) No, a much simpler explanation would suffice.

It is wonderful that we know a lot about ospins and how they work in vision. Where do they come from? Do these occur naturally in the probiotic state? Well, no. They are manufactured in a highly complex, miniaturized, information driven factory. Where did that come from? Where did the first biological information come from? Nobody knows. But for the evolutionary narrative, just pull the ospins out of the Darwinian hat, and begin the narrative from there.

All the articles cited begin with the assumption of evolution, weave the evidence into a “just so story,” and then end with the conclusion that since this evidence can be woven into a circular evolutionary “just so story,” it is evidence for evolution. The conclusion—evolution-- is the same as the hidden assumption—evolution-- built into the premises .

The articles are astonishingly void of details, full of “must have,” “may have”—blind assumption piled atop of blind assumption. The explanatory power is vastly underwhelming. The only reason to accept anything in these articles is that they came from “experts” who must know more than we do. And of course, all this is hidden in the inaccessible distant past, millions of years ago, so we can claim knowledge of what happened back then with impunity. As one posting stated something like this, “A lot of evidence goes missing over millions of years.” You betcha. If the evidence isn’t there, it was. It is just missing now. So the assumption is that there was evidence, again beginning with the assumption that evolution is true.

One has to first affirm evolution, then every piece of data, however remotely connected, becomes evidence for evolution—and at least as easily for intelligent design. But not to worry, because intelligent design is ruled out as a scientific explanation because it is not a naturalistic explanation—an inviolable rule imposed by naturalists by which science must be done.

In another post, we are told that paleontology provides evidence for the evolution of the eye. But paleontology can only illustrate homology (organs that appear to look the same) and homology can tell us nothing about genetic relationships. As we have already discussed, eyes that evolutionists previously claimed were related using homology are now known to be unrelated genetically. So to be honest, there is no “evidence” for the evolution of the eye from paleontology.

But then again, the articles were written by “experts.” So only the ignorant will reject their conclusions.

Well, we now know a lot about how eyes are made. There are information driven miniaturized factories that make the components from plans embedded in the genome. There is information in the genome for the assembly of the parts. And for the repair of the parts. And the plans for the components and assembly of the factories are contained in the information in the genome.

So there you have the machine shops and plans. In every situation where we can trace information, machine shops and plans to their origin, we find engineers. There is the pretty simple explanation that works unless you reject all but materialistic explanations.

So sorry, no “mistake” or “180 degrees.” Now please help us “non-believers” with a similarly simple and sensible explanation of evolutionary origins for the eye.

That you (or someone in this forum) think that a cookie is a suitable analogy for an eye makes me wonder how deeply that person understands biology.

But of course, neither the cookie nor the factory were used as analogies for the eye. They were both used in illustrating the level of explanation that would be acceptable or at least helpful in showing how an eye evolved.

In the cookie case, it was a red herring to basically assert that the level of explanation a creationist requires is absurd.

In the factory illustration, I was essentially requesting a very simple explanation. Think of how simple Henry Ford’s Greenfield Village assembly plant is. A simple explanation, not a simple eye.

Although eyes themselves often don’t fossilize well, we can readily trace the evolution of the eye by looking at the range of examples. Several chemicals are light-sensitive, including various proteins, which have a wide range of other functions. Having merely an ability to detect light versus dark is useful to many organisms for many purposes. Such simple light-sensing ability is widespread in animals, and genetic similarities support the idea that that basic level of light sensitivity, inherited from the common ancestors, was the starting point for the more complex eyes found in various types of animals. Different types of animals evolved complex eyes along different paths. This is perhaps most obvious when we look at insect eyes, with the very different approach of compound versus large lensed eyes. However, the large lensed eyes of mollusks have many distinctive features and developmental patterns that point to an independent origin from a basic eyespot.
Cephalochordates have a very simple eye, plausibly similar to the starting condition for vertebrates. Hagfish likewise have a quite basic eye. Having an eyespot (or two or more), rather than merely generalized light sensitivity across the body surface, allows some detection of directionality - there’s light ahead or behind. It might even be enough to have some detection of motion - knowing if something is moving towards you or you are moving towards something is often useful information. Often, eyespots are somewhat depressed, not just a flat spot. Again, this helps with detecting direction and might give a little protection to the structure as well. From a simple eyespot, increasing the number of light-sensitive cells improves light detection ability. Mutations in the light-sensitive molecules allow detection of different types of light, such as distinguishing colors. Increases in nervous system complexity enables processing more data from the light-sensing structures (although box jellies, with a quite simple nervous system, have well-developed eyes). If the eye evolves from a depressed spot on the surface to a cup with a very narrow opening (as in nautilus), it can function as a pinhole camera and produce images. Fill that cup with a transparent structure, or cover the eye with a protective layer, and you can get a lens, another way to make images. Seeing images enables a wide range of visual information and communication. In turn, improving the vision abilities has obvious benefits. Yet less good eyes are still quite functional. I couldn’t read a word on this screen without my glasses, but I could avoid crashing into large objects if I didn’t have the glasses. The evolution of the eye is a terrible example of supposedly irreducible complexity, because every step of the way is useful.

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Most mutations have no significant effect. Many mutations have small effects on the activity of proteins. Whether increasing or decreasing the activity of a particular protein matters, and if so, which is good, depends on the exact situation. A few mutations have large effects; these may be beneficial or harmful to the organism, but again benefit or harm is also very much a function of the particular situation.

The myth that mutations are overwhelmingly harmful reflects the fact that relatively few mutations are obvious. Also, any organism is reasonably functional in its current niche. Changes in something that already works are often not likely to make it better, and may easily make it worse. (Are any software engineers or government regulators listening?) But facing a new situation, change is often a necessity. Conversely, if conditions are particularly low-stress, it may be easier for sub"optimal" individuals to survive and perhaps be a step in a new direction. If a mutation is harmful enough, the organism with it dies and that mutation gets nowhere. So there’s a strong selective force that tends to eliminate the particularly bad mutations and support the spread of helpful ones.

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That’s not how it works.

What we see is eyes fall into the predicted nested hierarchy. That is why scientists are confident that they evolved. Evolution is not assumed. We conclude evolution because of evidence like the nested hierarchy.

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Ok, which mutations caused horizontal tailed fish? Vertical tailed fish? What caused some animals to have prehensile tails? Any such change so as to create a new kind would take so many changes, that they could never happen in time or in a sequence to actually happen.

No, you have some observations and are matching a few odds and ends where they look similar but don’t necessarily mean anything.

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