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Understanding Evolution - Development of Eyes

Well, I just had an answer 'disappeared' on Quora. Since I kind of liked it, I'm going to repost it here, to make sure it's still easy to find. I made a few minor edits, plus added a whole brand new figure to help with the explanation. Here is my answer to the question of:

If evolution is true, why aren't there millions of creatures out there with partially developed features and organs?
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To give one concrete example, let's take a look at eyes:

Mollusc Eyes
(Image Source: StephenJayGould.org - futuyma_eye.gif)

None of those eyes are hypothetical. Every single one is a diagram of an eye from an existing, living organism, all of them snails, actually, and every single one of those eyes is beneficial to its owner. And each one of those organisms is the end result of all the evolution leading up to it.

So, let's look at that first eye. It's the simplest. It's basically a light sensitive cup. Even if it doesn't let its owner form an image, it still lets those snails detect light, and the direction the light is coming from. Many, many millions of years ago, an eye very much like that was the most advanced eye that any snail possessed. But, evolution is a branching pattern. Once a population splits into two species that can no longer interbreed, there's no more sharing of genetic mutations or adaptations between the species.

So, that ancient species of snail with that cup type eye split into two species, and those split into more, and those split into more. In at least one of those lineages, by chance, the mutations appeared that made the eye more closely resemble that second eye in the diagram above. But all of its cousins species still had the simpler cup type eye. And all those cousin species with the simpler cup type eyes were still doing a good enough job of surviving and reproducing in their own niches, so they still survived. The new species with the 'better' eye probably had advantages in certain niches, especially those that required being more active, and so probably did pretty well for itself, and proliferated into its own group of species with those 'better' eyes.

Well, a similar process repeated again. At least one lineage in that new group got the mutations to make an eye with even better imaging capabilities. Its cousins with the type 2 eye still had their own niches where they survived, as did its even more distant cousins with the type 1 eye. And this repeated over and over again, until you ended up with the existing variety of snails we have today, with eyes ranging from that very simple cup eye to 'camera' eyes with lenses.

Here's a hypothetical, and overly simple, family tree of how this might have happened (you can do searches for snail phylogenetic trees to find some real ones). Imagine that the colors represent snails with a certain type of eye. Black is the original cup type eye. Blue is the type 2 eye. Red is the type 3 eye. And on through green, magenta, and cyan. Note how once a lineage evolves an eye, it's the only lineage with that eye*. For example, once the type 2 eye evolved in a single species of snail, only descendants of that species had type 2 eyes, because they were the only ones that could inherit it. It couldn't share that trait with its cousins. Also, snails with the original type 1 cup type eyes didn't all of a sudden all go extinct, and continued to evolve in their own lineages.

Hypothetical Snail Family Tree
Hypothetical Overly-Simple Snail Family Tree
Image Sources: David Peters Studios and StephenJayGould.org, with some editing on my part

And keep in mind, eyes are only one feature of snails. The living snails with the cup type eyes have still been evolving since that ancient ancestor, and have changed in other ways. They just haven't acquired the mutations that would have changed their eyes. Or more precisely, they just haven't acquired mutations to make their eyes better at resolving images. They may still have had other mutations affecting their eyes, such as light sensitivity.

So, do the existing snails with cup type eyes have a 'partially developed' organ? Well, I guess in one sense they do, because we know that an ancient animal with a similar type of eye eventually gave rise to descendants with a more complex camera type eye. But it's not 'partially developed' in the same sense as a half built bridge that can't ferry traffic. It's a perfectly functional eye that serves a purpose and is beneficial to the snail. And there's no guarantee that any of its future descendants will necessarily develop any of the more advanced eyes.

That's how it is with every organism and every feature on the organism. As long as we manage to escape extinction, we will all evolve in the future, from us humans to ants to dandelions (as populations - individuals don't evolve). Some of our existing features and organs will change. So, with the benefit of hindsight, those future organisms (at least the ones smart enough to be thinking about evolution) will be able to look back to how we are now, and recognize which of our now existing organs were only 'partially developed'.

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*Saying that common traits never appear in separate lineages is actually a little bit of an oversimplification. For traits that are more likely to evolve, they may evolve more than once in more than one lineage, in a process known as convergent evolution. However, the traits will have evolved independently, since separate lineages can't share DNA**. Additionally, the genetic basis will almost always be different, since it was separate mutations in the separate lineages that led to a similar structure. And the traits themselves may only be superficially similar. As a good example relevant to this essay, us vertebrates have also evolved camera type eyes. But, as you would expect given that we evolved them independently, the similarities are only superficial, and there are some very fundamental differences between our eyes and mollusc eyes.

**Okay, that's a little bit of an oversimplification, as well, but horizontal gene transfer is exceedingly rare in multicellular organisms.

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For the full story of what happened to my Quora answer, it wasn't anything malicious - it was the result of Quora's policy of merging similar questions. I had already answered one question, If theory of evolution is true, why aren't there more semi-evolved species with hands coming out of their skulls or other half-baked monstrosities?, and even adapted it to an entry on this site, Understanding Evolution - Origin of Limbs. Well, someone went and asked a similar question, If evolution is true, why aren't there millions of creatures out there with partially developed features and organs?. I wrote up an answer, looking at it a little differently than I had the first time. When someone noticed that both questions were similar, they merged the questions. Since Quora's policy is to only have one answer per user per question, when the questions were merged, they took my most popular answer and kept that. So, my newer answer more or less disappeared, and is basically only available by direct link or through my profile.

For a slightly different perspective, to quote my summary from my other answer, "evolution doesn't have foresight or a plan. For that matter, it's not a conscious entity at all, even if anthropomorphizing sometimes helps to explain it. Evolution only works through small incremental changes, and each of the changes has to be beneficial if the organisms are going to survive and pass those changes on to future generations. Every organism alive, past and present, is in a sense the end result of all the evolutionary history leading up to it. But in another sense, as long as they don't go extinct, evolution never stops, so every organism is also a transitional form to whatever its descendants might be."

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