Re: Origins of vision

I’m doing another repost, this time taking from an article I did about the origins of vision. Note that the quote coloring is reversed from how it normally appears.

Vision likely originated as simple eyespots in simple organisms. It also is traced back to jellyfish and their own simplistic eyespots, which are actually still present in some manner today. That is, jellyfish have areas of photoreceptor cells which don’t allow vision as we know it (they don’t even have brains), but they do allow a sensation of particular wavelengths of light to be perceived. These wavelengths often indicate depth (and maybe predators), which in turn may indicate food source (pelagic jellyfish don’t tend to get to plump).

Recent research has discovered the genetic pathway involved in light sensitivity in a close relative of the jellyfish.

“We determined which genetic ‘gateway,’ or ion channel, in the hydra is involved in light sensitivity,” said senior author Todd H. Oakley, assistant professor in UCSB’s Department of Ecology, Evolution and Marine Biology. “This is the same gateway that is used in human vision.”

This allows for a prediction using evolution: all organisms alive today which share a common ancestry with hydras will share this same genetic gateway. Organisms like flies, as the article points out, do not share this ancestry with vertebrates and as such do not share this genetic gateway. If they did share it, then wow. Creationists could actually trot out their improbability arguments.

“This work picks up on earlier studies of the hydra in my lab, and continues to challenge the misunderstanding that evolution represents a ladder-like march of progress, with humans at the pinnacle,” said Oakley. “Instead, it illustrates how all organisms — humans included — are a complex mix of ancient and new characteristics.”

(End different quote coloring.)

I looked this post up because I recently ran across a creationist who actually trotted out that old “the eye is irreducibly complex” bull and I was searching for some other links. But what’s interesting is what a different creationist was saying in the comment section:

You premised your claim of cnidarian relationship to vertebrates and humans on a gene they share in common. You said specifically, “This allows for a prediction using evolution: all organisms alive today which share a common ancestry with hydras will share this same genetic gateway.” I pointed out that certain beetles share certain genes with vertebrates and humans that other insects do not – and by your logic, that would mean these beetles share an ancestry with humans other insects do not.

As I pointed out at the time (and as the creationist failed to even come close to grasping), my claim was not based upon the sharing of individual genes, but rather on the sharing of complex genetic pathways. It is these pathways that ultimately allow for such a prediction. The creationist then confused the discussion on pathways with the article focus of a gateway. (I pointed out his error to him, but to no avail.) It is these pathways, by and large, which first get us to the point of where we can say that hydra and humans share a common ancestry in terms of vision. From that point we can look at the particular gateway in question and make the prediction I originally made. (One caveat: organisms which have lost their ability to see may not share the gateway.)

Neil Shubin inducted into NAS

This is satisfying:

The National Academy of Sciences today announced the election of 72 new members and 18 foreign associates from 15 countries in recognition of their distinguished and continuing achievements in original research…

Shubin, Neil H.; Robert R. Bensley Professor and associate dean, department of organismal biology and anatomy, University of Chicago, Chicago

Shubin is most famous for his evolution-utilizing research into Tiktaalik. I’m glad to see him inducted.

And congratulations to everyone else who was deemed worthy to be a member of such a prestigious institute.

Butchering science

Creationists hate science. They hate its conclusions, they hate its methods, they hate that it doesn’t support their silly beliefs. It’s that hatred that motivates them to butcher scientific articles and papers.

One recent butchering comes from Jack Hudson. I’m sure regulars here remember him. If not, it isn’t important. He’s a creationist with a background in introductory biology courses from 20 years ago. It’s doubtful he has much experience reading scientific papers, but that doesn’t stop him from trying.

In his post he butchers two articles. I’m going to focus on the first one, but I’ll briefly mention the second one. In that one researchers found that some negative mutations don’t change the protein sequence yet they are still negative. This one is simple. The entire sequence of a gene is not devoted to just the protein sequence. A mutation can therefore change one aspect of a gene without changing another – but it can still change another process that is important in forming proteins. Alter shape in one place and you have a good chance of seeing change somewhere else as a result. Biology is still all about shape.

The second paper, though. Woo. What a doozy of a butchering. First let me summarize the paper.

In asexual populations alleles can become fixed rather quickly. Their evolution is more straight forward because they aren’t mixing and matching genes. They produce offspring with the exact same genome, less there be a mutation. If there is a mutation, it can become fixed because things are generally less complicated with asexual populations and thus more black and white. Is this mutation good or bad? As the paper says and as Jack repeats upon hearing the term for the first time, alleles sweep through a population.

But when it comes to sexually reproducing populations, things become more complicated. And this is what the paper is about. The question is, do alleles sweep through populations in sexually reproducing populations like they do in asexual populations? The answer is no.

Now, if we’re to believe Jack, this means that evolution has failed because, why, evolution predicts an advantageous allele to reach 100% fixation, of course. Except it isn’t so black and white with sexually reproducing populations. (Nor does evolution predict that anyway.)

What the researchers did was study over 600 generations of fruit flies. They let them breed naturally, but then selected out the eggs which were produced the most quickly. This led to significantly faster reproducing populations. They then tracked specific alleles to see if they would become fixed. What they found was that they don’t.

Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.

The conclusion here is that selection for a particular trait in sexually reproducing populations acts upon many different aspects and genetic variants within the genome, not merely a single gene or SNP.

This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.

This is the actual conclusion of the paper. To put it another way (and to repeat myself), advantageous variants do not wipe out other genetic variants in a sexually reproducing population, instead acting on variation in a more subtle and complicated way. The big conclusion here is that there is a difference in how genes become fixed (or not fixed) in asexual populations versus sexually reproducing populations.

And Jack’s conclusion?

In short, if the activity failed to occur in the lab under optimal conditions, it is unlikely that traits are going to be transmitted this way in nature.

The traits are still being transmitted through natural selection working on variation. Jack’s conclusion has little to no connection to anything from the paper. In fact, it is abundantly clear that he read an article somewhere, figured out how to butcher it, and then went and read a few lines from the original paper.

I’ve said in the past that what takes a creationist 30 seconds to say takes an educated person 3 hours to correct. This post and the research required for it didn’t take that long, but the sentiment remains true – it’s a real hassle to untangle the carelessly mushed writings of a creationist.

Repost: Only in the light of evolution

There are two reasons I want to make a repost of a post from about a year and a half ago. First, it’s always interesting to go back and read old posts for me. From time to time I have no recollection of making a certain post, so when I see it, it’s almost like it’s brand new to me. I do happen to remember this one very clearly, but it is at least understandable why I was skimming posts from May 2009. Second, I average significantly more views now than I did a year and a half ago. I feel this post is a pretty important one, and now that more people can see it, I would like to throw it back up.

~~~

I am following a specific chapter in Jerry Coyne’s Why Evolution is True.

The fossil record: We should see fossils in a certain order if evolution is correct. They should go from simple to more complex overall, and the fossils we see in the most recent strata should resemble extant life much more than the fossils we see in old strata.

We should also see changes within lineages. We should be able to observe instances of gradual change in species that eventually leads up to either current species or at least to the time of extinction for these species.

Here’s a simple timeline of life’s history. Click it.

What the evidence shows is gradual change. First we find simple bacteria which survived off energy from the Sun, then we see more complicated cells known as eukaryotes arise. (You are a eukaryote.) Next we see a slew of multi-cellular animals arise. They’re still simple, but much more complex than the original bacteria. A few million years later more complicated life arrives. Early (and simple) plants begin to take hold. Soon the fossil record begins to show more plant complexity with low-lying shrub such as ferns, then conifers, then deciduous trees, and finally flowering plants. Gradual changes occur in the oceans and fresh waters which lead to fish and then tetrapods (Tiktaalik comes to mind).

One of my favorite fossils is trilobites. They’re extremely common due to their hard bodies. In fact, even their eyes are well-preserved because of their hard mineral make-up. I personally recall entering touristy-stores seeing countless fossils of these guys in the mid-west to the west (which, unsurprisingly, was once a shallow sea). This image shows the different lineages of this organism. Studies show that the ‘rib’ count has changed over time in each individual species, often without regard to how the other species changed. Going back further, there is less and less divergence in each species. Eventually, as evolution predicts, they all meet at a common ancestor.

So naturally the next step is to find fossils which show more significant changes. Let’s take birds and reptiles. They hold similarities between each other, both morphologically (certain shapes and structures) and phylogenetically (genetic sequence). A good hypothesis is that they came from one common ancestor. If this is true, the links between birds and its ancestors and reptiles and its ancestors should lead to the same point. They do. Dinosaurs are the ancestors of both. The links between birds and dinosaurs are so incredibly well established that I’d prefer to not go over them in detail. But for starters, some dinosaurs sported feathers and claws and had the same proteins for the feather-making process as extant birds. The links between reptiles and dinosaurs is easier just on intuition, so I’ll leave it at that for now.

Other transitional fossils include the already mentioned Tiktaalik. A view of the history of life can be see here. This shows the change in head and neck structure. Recent research on long-ago discovered Tiktaalik fossils has shown the importance in the gradual bone changes in the neck. These changes – a hallmark of evolution – were important to the ability to turn its head. This is a hallmark because natural selection only modifies what already exists. This is precisely what happened.

Going further with this example, evolution makes predictions as to how early fish evolved to survive on land. If there were lobe-finned fish 390 million years ago and obviously terrestrial organisms 360 million years ago (which is what the fossil record shows), then if scientists are to find transitional fossils, they should date in between that time frame. There should be an animal that shows both features of lobe-finned fish and terrestrial animals. Tiktaalik is that animal. It has fins, scales, and gills, but it also has a flat, salamander-like head with nostrils on top of its nose. This is a good indication that it could breathe air. Its eyes were also placed there, indicating that it swam in shallow waters. Furthermore, it was lobe-finned, but shows bones (which eventually evolved into the arm bones you used to get out of bed today) that were able to support its weight to prop itself up. And of course, it dates to 375 million years ago.

Next, evolution says the fossil record should show recent fossils being more closely related to extant species than are early fossils. This is precisely what happens. Sixty million years ago there were no whales. Fossils resembling modern whales only show up 30 million years ago. So, again, evolution makes a predication: if transitional fossils are to be found, they will be within this gap. And so it is.

We begin with Indohyus. It was an artiodactyl. This is important because extant whales have vestigial bones which indicate that they came from this order: scientists expected to find this because, again, evolution predicted it. It should be of no surprise that this fossil dates to about 48 million years ago, right in the predicted gap. From here there is a gradual evolution shown in the fossil record which leads up to modern whales.

Unraveling black widow silk

I no longer find it amazing how much of a basis evolution forms in various bits, pieces, and even chunks of research projects; it is expected.

Thought of the day

The only thing which can (and does) correctly explain all the dinosaur fossils of Utah and the rest of the world is evolution.

Weird pets

I was reading about the Canada lynx on Why Evolution is True and that got me thinking about all the weird pets people have.

First up are skunks. It’s unfortunately illegal to keep them as pets in some states (including Maine), but where it is legal, an owner can have their skunk’s scent glands removed so they don’t spray all over the place. They’re expensive to keep (needing a weird diet consisting of food better than what a lot of humans eat) and they’re apt to get into everything, but they’re known to be very friendly.

The closest I’ve come to a pet squirrel was one that used to come up to the porch for peanuts. Unlike all the other squirrels, he (or maybe she) wouldn’t run away when someone opened the door. He’d stick around, knowing food was likely coming his way. He stuck around for a few seasons, presumably dying two or three winters ago. (Squirrels can live up to 10 years in captivity, but tend towards 4 years in the wild.)

I don’t know much about raccoons, but the fact that they make me think of little train robbers when I see them forces me to include them.

The red fox is relatively commonly tamed. In fact, one well known experiment in Russia has consisted of researchers grouping individual red foxes by how friendly they are towards humans and then selectively breeding those individuals who display the most friendly tendencies. It has resulted in very dog-like animals; the foxes (now called the domesticated silver fox) wag their tails in excitement, whimper when left alone, and have lost their normal coloring pattern (the researchers did not select for color). Just like with all artificial selection, it’s a good example of evolution in action.

But even when decades of selection haven’t been taking place, the red fox still manages to be a decent, tamable pet.

The basics

Here’s a good video on some basics of evolution. Just try to get by the narrator’s weird way of saying “genome”.

Australopithecus sediba

Australopithecus sediba is a recent discovery of a new species that represents intermediate features of modern day humans and Australopithecus africanus. The discovery includes two well-preserved fossils dating back 1.95 to 1.78 million years ago, showing a mosaic of human and A. africanus characteristics. It is likely a descendant of A. africanus.

These new fossils, however, represent a hominid that appeared approximately one million years later than Lucy, and their features imply that the transition from earlier hominids to the Homo genus occurred in very slow stages, with various Homo-like species emerging first.

“It is not possible to establish the precise phylogenetic position of Australopithecus sediba in relation to various species assigned to early Homo,” wrote Lee Berger, a lead author of one of the Science reports. “We can conclude that… this new species shares more derived features with early Homo than any other known australopith species, and thus represents a candidate ancestor for the genus, or a sister group to a close ancestor that persisted for some time after the first appearance of Homo.”

Again, the new species is considered to likely be a descendant of A. africanus, but whether or not it is part of human lineage is less certain. Importantly, however, it represents at least a cousin that was evolving alongside our ancestors. (Phylogenetic relationships, in fact, are often based upon indirect ancestry.)

For more of the details about this discovery (such as the fact that it was bipedal or just how it was all so well-preserved), give Brian Switek’s post a look.

Australopithecus sediba

Australopithecus sediba is a recent discovery of a new species that represents intermediate features of modern day humans and Australopithecus africanus. The discovery includes two well-preserved fossils dating back 1.95 to 1.78 million years ago, showing a mosaic of human and A. africanus characteristics. It is likely a descendant of A. africanus.

These new fossils, however, represent a hominid that appeared approximately one million years later than Lucy, and their features imply that the transition from earlier hominids to the Homo genus occurred in very slow stages, with various Homo-like species emerging first.

“It is not possible to establish the precise phylogenetic position of Australopithecus sediba in relation to various species assigned to early Homo,” wrote Lee Berger, a lead author of one of the Science reports. “We can conclude that… this new species shares more derived features with early Homo than any other known australopith species, and thus represents a candidate ancestor for the genus, or a sister group to a close ancestor that persisted for some time after the first appearance of Homo.”

Again, the new species is considered to likely be a descendant of A. africanus, but whether or not it is part of human lineage is less certain. Importantly, however, it represents at least a cousin that was evolving alongside our ancestors. (Phylogenetic relationships, in fact, are often based upon indirect ancestry.)

For more of the details about this discovery (such as the fact that it was bipedal or just how it was all so well-preserved), give Brian Switek’s post a look.