Science & Nature Archive

Wednesday, March 22, 2017

Understanding Evolution - Development of Eyes

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.

I wrote a Quora answer that I thought was a good explanation on how complex features can develop. The answer was dropped from their main archive when the question was merged with a similar one I had already answered. Since I thought it was a good explanation, and to make it more accessible, I'm going to repost it here. 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?

To give one concrete example, let's take a look at eyes:

Mollusc Eyes
(Image Source: - 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, 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'.


*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.


For a slightly different perspective, read the related entry, Understanding Evolution - Origin of Limbs.

Want to learn more about evolution? Find more at Understanding Evolution.

Updated 2018-02-07 - Simplified much of the extraneous commentary that didn't have to do with the body of the entry.

Friday, March 17, 2017

Understanding Evolution - How Humans and Apes Fit Into the Tree of Life

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.

I came across a question on Quora the other day that seemed to reflect a common incomplete understanding of evolution, If it took 5 million years for today´s humans to evolve from the apes, how long time did it take for today´s apes to evolve from their origin?. There are a few issues with that question, but rather than enumerate them all here, I'll just jump into the explanation, which will hopefully make it clear as we go. The one thing I'll say up front is that we diverged from chimps & bonobos more like 6 million years ago, not 5 million.

It all depends on what perspective you want to take, and which starting point you want to go with. When people bring up the 6 million years for humans to evolve from apes, what does that really mean? Take a look at this diagram:

Hominid Evolutionary Tree
Click to Embiggen
Image Source: The Open University - Studying mammals: Food for thought

That's one probable evolutionary tree for us over that time (the exact details are subject to debate). Notice how bushy it appears. Populations kept on splitting and splitting and splitting, and most of those species ended up going extinct. We're the only surviving members of that lineage (though Neanderthals nearly made it to the present day). But, if you wanted to ask, how long did it take for humans to evolve, where would you pick as your starting point in that diagram? It just happens to start with Orrorin tugenensis, but that's only because that's where that artist decided to start it. They could just as easily have started with Ardipithecus ramidus, and you could say it took us 4 million years to evolve from that. Or, they could have skipped ahead and started at Homo habilis, and you could say that it took us 2 million years to evolve from that. Or, you can notice that Australopithecus boisei and us are pretty distant cousins on that tree. If A. boisei had managed to not go extinct, or to have left descendants that kept on evolving into some new species, there might be another ape alive right now more closely related to us than chimps and bonobos. So, then we might be saying that it took us 3 million years to evolve from apes. But it wouldn't be anything different about how we evolved - it would just be the fact that we had a still living closer cousin to compare ourselves to. (Note that that terminology is a bit misleading, as you'll hopefully understand after reading this full entry - we are simply apes ourselves.)

Here's another diagram, this time including the still surviving great apes, but not showing all the ancestors or extinct species from side branches that died out:

Ape Evolutionary Tree
Click to Embiggen
Image Source: - Milestones of Human Evolution from Paleontology & Bioinformatics

That's where the 6 million year number comes from. It means that 6 million years ago, there was a population of animals whose descendants would eventually become chimps, bonobos, and humans. It was the last common ancestor of us three surviving species. It took each of our species 6 million years to evolve from that population. But recall the branching pattern from the previous diagram. It wasn't a straight line from that population to each of us species that's still around. It split and split and split in a bushy pattern. In the lineage that led to us, only one species survived to the present - us. In the lineage that led to chimps and bonobos, those two species survived to today.

And you don't have to pick just chimps and bonobos. If you look at gorillas, our common ancestor with them was alive roughly 8 million years ago. So, it took 8 million years for gorillas to evolve from that ancestor. It took chimps 8 million years to evolve from that ancestor. It took bonobos 8 million years to evolve from that ancestor. And it took us humans 8 million years to evolve from that ancestor. Chimps, bonobos, and us share a common portion of that 8 million years. Chimps and bonobos alone share an even longer common portion. It would be similar to asking, how many generations did it take to get from your great-grandparents to you, or to your brother, or to your cousin, or to your second-cousin? In all cases, it would be three generations. For you and your brother, you'd share most of that lineage, starting with your great-grandparent, then your grandparents, and then your parents. With your cousin, you would only share your great-grandparents and grandparents. And with your second cousin, it would only be your great-grandparents. There are a lot more greats than that considering our evolutionary history, but it's the same concept. We share more of our lineage with chimps and bonobos than with gorillas. And we share more with gorillas than with orangutans. And we share more with orangutans than with non-apes.

If you want to go further and ask how long it took for apes to evolve, it really depends on how far back you want to go. Here's another diagram:

Primate Evolutionary Tree
Click to Embiggen
Image Source: ResearchGate

Now, we get into a problem of semantics. In language, apes have a name to describe them as distinct from monkeys. But we're not really a completely distinct group. To have a distinct group in classifying these types of things, all members of that group should share a common ancestor that no other group can claim in its ancestry. Apes have such an ancestor around 20 million years ago. The only descendants of that specific animal are apes. But monkeys don't have that type of unique common ancestor. There's no single ancestor of 'monkeys' that isn't also an ancestor of apes. We're not two separate groups. Us apes are really just a specialized subset of monkeys without tails. But, if your question is just when 'apes' first appeared, then like I already said, the last common ancestor of all apes was alive around 20 million years ago.

But why stop there? When biologists say that all life on earth is related, they mean it. All life on earth shares a common ancestor. If you go back far enough, you can find our last common ancestor with chipmunks (~90 million years ago), or with a triceratops (~320 million years ago), or with a goldfish (~432 million years ago), or with an apple tree (~1.6 billion years ago), or even with the streptococcus bacteria that may have given you your last sore throat (~4.3 billion years ago). So, if you want to start at the beginning, you have to figure out when our earliest, earliest single celled ancestors were alive. The problem is that it's hard to find evidence of things that nearly inconceivably ancient, but it was probably more than 4 billion years ago. So, in that sense, it's taken humans over 4 billion years to evolve. It's take starfish over 4 billion years to evolve. It's taken e. coli over 4 billion years to evolve. It's taken oak trees over 4 billion years to evolve. Etc. Etc. Every organism alive is the end result of all that evolution leading up to where it is now.

Complete Evolutionary Tree
Click to Embiggen
Image Source: evogeneao Tree of Life

So to summarize, it's taken chimps, humans, and bonobos roughly 6 million years to evolve from our last common ancestor. It's taken all of us apes as a whole roughly 20 million years to evolve from our last common ancestor. You can keep going back in our ancestry until somewhere more than 4 billion years ago to the first life, that was the ancestor of everything alive today.


There are some really good trees of life and similar type pages to play around with. Here are a few (I already linked to one above, but it's worth repeating). They mostly include only the tips of the tree for organisms that are still alive. So, you won't necessarily be able to find an Australopithecus or a Tyrannosaurus, but even just sticking to living animals, it's a huge, huge tree.

Want to learn more about evolution? Find more at Understanding Evolution.

Sunday, February 12, 2017

Understanding Evolution - Balancing Selection Pressures, Or Why All Features Are Tradeoffs

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.

Gazelle & Cheetah DioramaTo celebrate Darwin Day, I'm going to recycle a recent Quora answer about evolution. Somebody had asked, Why would a gene that makes a gazelle slightly faster, but still much slower than a cheetah be favored by evolution?. Here's my answer.


Because everything in life is a trade-off, and cheetah attacks aren't a gazelle's only concern.

Running faster comes at a cost. In particular, it means bigger or stronger muscles to be able to propel yourself faster. Bigger muscles take more food to grow, and more food to maintain. So, the fastest gazelle is also the most likely to starve in times of scarcity. And it's also putting more of it's food resources into those muscles instead of reproduction and/or nurturing young, and may end up not having as many offspring / surviving offspring as a slightly slower gazelle.

And gazelles have other predators besides cheetahs. One in particular is so efficient that it doesn't really matter how fast a gazelle runs - our bullets are faster. And which animals do trophy hunters target? The biggest and most impressive. It's already been documented that trophy hunting has led to bighorn sheep having horns that aren't so big ( - Intense trophy hunting leads to artificial evolution in horn size in bighorn sheep), and that size limits in fishing has led to smaller fish ( - Intensive fishing leads to smaller fish). I don't know if gazelles have been studied in this manner, but I wouldn't be surprised at all if human hunting had strong selection pressures on their sizes.

There's this whole complex network of selection pressures acting on gazelles (and all other organisms). Evolution has to balance (metaphorically since evolution isn't conscious) an organism's strategies to dealing with these pressures, and can't focus on optimizing completely for one selection pressure if it means compromising too much on other ones. So, cheetah attacks are one pressure on gazelles, and this particular pressure pushes gazelles to be faster. So, evolution pushes them to be fast enough to greatly lower their likelihood of being caught by a cheetah. But going even faster would only reduce that risk slightly, and at the cost of hurting the gazelles chances of survival/reproduction in other ways. So, gazelles are fast enough, and there's no reason to waste their limited food resources on even bigger muscles, when they could be using those resources for other activities, or even just being smaller so that they don't need as much food.


If you want to look at it another way, it's like wondering why everybody doesn't have a Ferrari. Sure, Ferraris are fast, but they're also expensive, use a lot of gas, and have many compromises that make them less than practical everyday drivers. Evolution could make gazelles faster, but only by compromising them in other ways.


To add one more thing - the reason gazelles just have to be reasonably fast, but not as fast as or faster than a cheetah, has to do with the way attacks actually play out in real life. As Brian Dean pointed out in his answer, it's not like a track race, where the fastest organism is the winner. Cheetah's are only sprinters, with limited stamina. Gazelles are keeping a lookout for cheetahs already, trying to make sure the cheetahs don't get too close. The usual result is that the cheetahs can only get so close before starting their sprint, meaning the gazelles have a head start. The gazelle only needs to be fast enough that it can avoid the cheetah until the cheetah gives up, which is still pretty fast, but a good deal less fast than a cheetah. And an extra few miles an hour on the gazelle's top speed is a sizable percentage difference in how much more time it has to evade the cheetah.

Image Source: Wikimedia Commons

Want to learn more about evolution? Find more at Understanding Evolution.

Sunday, February 12, 2017

Happy Darwin Day 2017

I'm cheating. This is mostly copied from last year with just a few updates.

Darwin's BirthdayToday is Darwin Day, the 208th anniversary of Charles Darwin's birth. To quote one of my previous Darwin Day posts, Charles Darwin was "the man who presented evolution in such a way and with sufficient evidence that it became obvious that it was the explanation for how life developed on this planet. Others had ideas of transmutation before Darwin, and Alfred Russel Wallace even came up with a theory of natural selection very similar to Darwin's at around the same time, so it's apparent that humanity would have eventually recognized how evolution works. But Darwin's genius in presenting all the evidence for evolution in the way he did certainly gave the field a huge head start."

If you want to see if there's anything specific going on in your neck of the woods, you can check out the list of events at, or my recent post. I couldn't find anything for Wichita Falls again this year. And I never did watch Inherit the Wind last year, so maybe I'll be able to talk my family into it this year.

To celebrate Darwin Day on this site, I'm going to provide links to a few of my previous entries. This first set of links is entirely to entries specifically relevant to Darwin or written just for Darwin Day.

And while I write way too much about evolution to list all of my evolution entries, here are a few highlights since the previous Darwin Day:

Friday, February 10, 2017

Upcoming Darwin Day Events

Darwin's BirthdayFebruary 12th is Darwin Day. Many organizations are planning events for this weekend to celebrate. You can check for events close to you. Here are a few from across Texas and Oklahoma (well, at least the ones you can still make it to - there were some events earlier this week).

Austin, TX - Center for Inquiry: Darwin Day 2017
Feb 11, 12pm - 5pm Details
Official Event Page
Facebook Page

"FREE event to celebrate the 208th anniversary of Darwin's birth. There will be something for everyone--fun learning activities for children and teens, fascinating lectures and trivia contest for adults, and professional development credit for teachers."

Tyler, TX - Darwin Day Tyler 2017
Feb 10, 5pm - 7pm
Feb 11, 10am - 4pm Details
Official Event Page
Art & Seek Details

"This year's Darwin Day celebration features four main events: two different public science lectures, evolutionary themed video screenings, and a teacher development workshop. There will also be other events for students of all ages at the Discovery Science Place, the University of Texas at Tyler, and Tyler Junior College.

All events are free of charge!"

Nagadoches, TX - Darwin Day at SFA
Feb 10, 1pm Details
Press Release

"The Stephen F. Austin State University Department of Biology will host its second annual Darwin Day program. The program will include a seminar by Dr. Charles Pence, assistant professor of philosophy and religious studies at Louisiana State University. Pence's seminar is titled 'Evolution and Chance: From Darwin to the Pioneers of Statistics in Biology.' "

San Antonio, TX - Trinity University: Panel Discussion on Darwin, Gender, and Race
Feb 15, 5pm - 6.30pm Details

"In celebration of Charles Darwin's 208th birthday join us for a discussion on Darwin, Gender, and Race. Four Trinity professors will provide a panel discussion of Darwin's views on gender and race, the current scientific views on race, and the contributions of minorities and women to evolutionary theory. Following brief introductory comments, the panel will open up for questions from the audience. Also be sure to check out the exhibit at the Coates Library, Third Floor: Who's studying evolution these days? A look at modern scientists; Feb. 8-15."

Norman, OK - Norman Naturalism Group: Darwin Day! Potluck and Speaker: The EVOLUTION of Religion
Feb 12, 5pm - 9pm Details
Official Event Page

"The Norman naturalism Group celebrates Darwin Day 2017 with a pot-luck dinner and speaker. The topic is "The Evolution of Religion". Pull out your best recipe and get ready for some more good eating and good talking."


Selling Out