The genius of Charles Darwin

By the time that an animal had reached, after numberless generations, the deepest recesses, disuse will on this view have more or less perfectly obliterated its eyes, and natural selection will often have affected other changes, such as an increase in the length of antennae or palpi, as compensation for blindness.

The above quote comes from On the Origin of Species. It is just one of the numerous instances where Charles Darwin, on the basis of his theory, makes a wonderful prediction that comes true so many years after the fact. In this case, his prediction has been shown to be true over and over; species which have gone millions of years in the dark lose their eyesight again and again. We see this especially in many species of cave fish, but it isn’t limited to the oceans:

With a leg span of only six centimetres and a body size of around twelve millimetres, the spider Sinopoda scurion is certainly not one of the largest representatives of the huntsman spiders, which include more than 1100 species. However, it is the first of its kind in the world without any eyes.

“I found the spider in a cave in Laos, around 100 kilometres away from the famous Xe Bang Fai cave,” reports Peter Jäger, head of the arachnology section at the Senckenberg Research Institute in Frankfurt. “We already knew of spiders of this genus from other caves, but they always had eyes and complete pigmentation. Sinopoda scurion is the first huntsman spider without eyes.”

One prediction the theory of evolution allows us to make today that Darwin couldn’t make in his lifetime is that the genes for vision in these now-blind species should exist but be broken. If they do not exist, then either there is some really funky timeline and divergence activity (that is, these are old lineages that evolved before their sighted brethren) and we should see a lot of other genetic differences or evolution just isn’t true. Neither one of those options is very likely, of course. What we observe instead is that, indeed, the genes for vision are a broken, jumbled mess. That isn’t the case yet for the above spider because, as far as I know, no such studies have been carried out, but it is the case wherever else these sort of species have had their genes analyzed.

One point I think that needs to be made sure with Darwin’s quote here is this: Natural selection is unlikely to be the only factor in the disappearance of eyes among these species*. In fact, it could have little to nothing to do with the process at all. Vision in the dark is a useless thing, so natural selection may obliterate it for the sake of saving energy or preventing potential injury to a sensitive body part, but I believe it is much more likely that it simply did nothing. It neither selected for nor against vision. As a result of the lack of positive selection, mutation and genetic drift took over and vision in these species simply faded away.

*I really have two points here. First is the one I just made in the above paragraph. Second is the fact that Darwin was referencing natural selection in regard to it creating some compensation for blindness, not in regard to it directionally causing the blindness.

GE Salmon may gain FDA approval

The FDA is considering allowing a company to market a fish that has been genetically engineered.

If the FDA approves the sale of the salmon, it will be the first time the U.S. government allows such modified animals to be marketed for human consumption. The panel was convened by the agency to look at the science of the fish and make recommendations on its safety and environmental impact.

Ron Stotish, chief executive of the Massachusetts company that created the salmon, AquaBounty, said at Monday’s hearing that his company’s fish product is safe and environmentally sustainable.

FDA officials have largely agreed with him, saying that the salmon, which grows twice as fast as its conventional “sisters,” is as safe to eat as the traditional variety. But they have not yet decided whether to approve the request, saying there is no timeline for a decision.

One of the chief concerns most people have about genetically altered food is that it contains DNA. I kid you not. That concern is more prevalent where cloned animals are in question, but it’s just as incoherent.

But there are more reasonable concerns.

Critics have two main concerns: The safety of the food to humans and the salmon’s effect on the environment.

Because the altered fish has never been eaten before, they say, it could include dangerous allergens, especially because seafood is highly allergenic. They also worry that the fish will escape and intermingle with the wild salmon population, which is already endangered.They would grow fast and consume more food to the detriment of the conventional wild salmon, the critics fear.

There’s really no reason to suspect any extra allergies. These fish are being caused to grow faster through the use of hormones they already regularly produce; they’re just producing more hormones than they would without the inserted gene and regulator. If someone doesn’t have an allergy as a result of these hormones now, they won’t have an allergy to these new salmon.

As far as contamination is concerned, I doubt there will be any intermingling, but if it does happen, it seems unlikely the new fish will out-compete the current wild population. Natural selection could act to increase the frequency of hormone production relatively easily. It hasn’t. It’s unlikely the new population would be more fit in the given wild population’s environment.

I foresee this getting approval, but it wouldn’t surprise me if the FDA acquiesced to critic’s demands and forced a ‘warning’ to be placed on the fish listing it as genetically altered. This would be unfortunate since there is no effective difference between eating a wild population salmon and a genetically altered salmon. But it’s the FDA. There will be an unnecessary warning added; it’ll probably be removed in 5-10 years when it becomes even more clear that this fish is very safe to eat.

Water on the Moon

NASA discovered there is plenty of water on the moon.

Experts have long suspected there was water on the moon. So the thrilling discovery announced Friday sent a ripple of hope for a future astronaut outpost in a place that has always seemed barren and inhospitable.

“We found water. And we didn’t find just a little bit. We found a significant amount,” Anthony Colaprete, lead scientist for the mission, told reporters as he held up a white water bucket for emphasis.

He said the 25 gallons of water the lunar crash kicked up was only what scientists could see from the plumes of the impact.

This is equivalent to roughly a bathtub’s worth of water from this double-impact.

One part of me wants to endlessly speculate at the possibility of microbial life. But all reason and rationality tell me to be cautious. Water does not automatically mean life (especially when its frozen).

…but what if it does mean life, at least in this case? Would the world realize the utter significance of this discovery? Not since Darwin described evolution by natural selection has there been such an important find.

Old eggs, daphnia, and evolution

When predation is high, crustaceans and other water loving egg lay-ers are not hatched much. What often happens is that they will remain dormant until later in the year when the predators are much less active. This offers a great research opportunity into evolution.

By hatching these eggs, Hairston and others can compare time-suspended hatchlings with their more contemporary counterparts to better understand how a species may have evolved…

What happens is that some of these eggs can remain unhatched for years and years, not just seasons. This is the case with daphnia. These are normally seasonal crustaceans, but researchers have specimens which are upwards of 40 years old. They use these to compare the change which has happened to this species over time.

In the 1960’s, the lake from which these daphnia were taken had non-toxic levels of algae. But in the 1970’s, pollution had caused the algae to raise to a deadly imbalance. Currently, daphnia still reside in the lake, but researchers have found they are markedly different from the eggs they hatched. The older version of the species was unable to survive in the lake, poisoned by the overwhelming cyanobacteria. Clearly, the newer species had adapted to their new environment throughout the 70’s and subsequent decades.

Only in the light of evolution

Now that finals are over, I can devote more time to my dear, neglected blog. I begin with a series:

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.

Ancestral environments and reverse evolution

There’s been a long debate regarding whether evolution can be reversed or not. The general trend has been that it can not. The idea goes that once one evolutionary pathway has been crossed, it cannot be retraced back to its origins. It turns out that is not entirely true.

Says [researcher] Henrique, ‘In 2001 we showed that evolution is reversible in as far as phenotypes are concerned, but even then, only to a point. Indeed, not all the characteristics evolved back to the ancestral state. Furthermore, some characteristics reverse-evolved rapidly, while others took longer. Reverse evolution seems to stop when the populations of flies achieve adaptation to the ancestral environment, which may not coincide with the ancestral state.

What the researchers did was subject fruit flies to various selection pressure for multiple decades, i.e., they changed their environment over and over. The ‘end’ result was fruit flies that were markedly different in their traits as compared to the original specimens. That’s evolution. Children should understand that. What happened next was the researchers mimicked the original environment of the fruit flies from decades gone by. In response, the fruit flies adapted to those environments, possessing many of the same allele frequencies they originally had. What I find particularly interesting is that they did not evolve exactly the same, but they still evolved in a way that was similar to the original phenotypes. This helps to explain why sharks and horseshoe crabs remain so similar for so long: the gene pool of the population centers around certain allele frequencies because, well, they work. Change may happen – in fact, it certainly does – but ancestral pheno- and genotypes can evolve to such similar future counterparts as to make little difference in show, even though we know there to actually be differences, at least in contigency. It’s a bit like how two people of very different backgrounds and even different alleles can come to have the similar tones to their skin. Their evolutionary contigency, or histories, are different, but the result is virtually the same.

Another point of note here is that evolution can produce similar things, but it will almost never produce the exact same thing. The history of life, if rerun, would be much, much different in all likelihood. When exolife is discovered, we’ll have indirect confirmation of this. Until then, it should be important for people to realize that nothing in biology is inevitable – including humans.