Weird pets

Posted on July 31, 2010 by Michael

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.

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Photolyase and cancer

Posted on July 28, 2010 by Michael

Upon arriving at the beach yesterday, I lathered on the sun screen. Being relatively fair-skinned, I’ve learned my lesson in forgetting or not using enough of the stuff, and I wasn’t about to get all burned up. I don’t like eating lobster; I certainly don’t want to look like one.

But that isn’t the only reason I throw the stuff on so heavily. I’m also well aware of the tenacity and, if such a word is appropriate, vulgarity of cancer. Tanning is just a bad idea unless someone really wants to be diseased. It may look good (and not always), but I doubt that has ever brought solace to any cancer patients. Laying out in the sun without protection (as I saw a few people doing all day – it was at least 85 F, not a cloud in the sky) or jumping in one of those tanning cancer tubes is a sure-fire way to cause potentially deadly somatic cell mutations.

The way this works is that UV light slaps into the double helix structure of DNA causing an incorrect fusion in base pairs on the same side of the helix. Imagine – and apologies for the violence of it all – getting punched in the mouth. Instead of your teeth vertically matching as they do now (at least relatively), a couple teeth on the bottom row are now horizontal and facing each other. This calls for a dentist.

Different organisms have different mechanisms (dentists) for correcting damaged DNA. Naked mole rats, for example, have two genes for contact inhibition instead of the single gene virtually all other mammals have. This has resulted in no one ever recording an instance of cancer in the ugly little critters. If humans had this mechanism, cancer probably wouldn’t be nearly the problem it is.

Instead we get a number of repair mechanisms, chief among them base excision, nucleotide excision, and mismatch repair. (The mechanism in naked mole rats doesn’t repair mutated cells; it merely stops them from proliferating.) Unfortunately, the repair fidelity, just like the copying fidelity, of DNA is not perfect. Mistakes are made, mistakes are missed. We get cancer.

Part of our plight arises from something we’ve lost over evolutionary time. Most plants and other animals have a protein called photolyase which specifically seeks out UV damaged DNA.

Researchers at Ohio State University were recently able to observe exactly how photolyases perform their protective duty. The photolyase protein captures energy from visible light and uses it to project a single proton and a single electron towards a dimer in DNA. The two tiny particles then initiate a series of reactions that knock the contorted nucleotides back into place across the ladder, without needing to remove them like normal human proteins do. A proton and electron finally return to the photolyase protein, presumably so it can dash off to fix the next dimer it finds.

In other words, this dentist isn’t very gentle. He just punches your contorted teeth back into position. (Okay, it’s more elegant than that, but I had to finish the analogy.)

The article goes on to speculate as to the potential utilization of this protein in humans.

Given that photolyases were lost in evolution, it was possible that other proteins in the cell that allowed photolyases to do their job were also lost. But mice that were given the gene for the photolyase protein showed remarkable protection from UV damage. This means that in mice, the rest of the cellular infrastructure that photolyases need is still there. Chances are good that it’s there for humans as well.

There are other instances of mice being able to utilize genes not otherwise found in them, almost as if they’ve had them all along. For example, when injected with snippets of DNA for making red photo-pigment, normally dichromatic mice suddenly had trichromatic vision. This indicates an earlier evolved ability to see colors in the mammalian line that was later lost. In all likelihood, the appropriate gene(s) was probably just turned off out of a lack of need, leaving in place much of the cellular machinery needed to utilize red photo-pigment. I suspect the same is true with photolyase. If this can be extended to humans, a significant leap in the fight against many skin cancers may be on the horizon.

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Eliot Cutler responds

Posted on June 23, 2010 by Michael

I’ve asked the three main candidates* to either state or clarify their positions on the teaching of creationism in public schools. Paul LePage acted like a spoiled little brat and deleted my question from his Facebook page. Libby Mitchell has yet to respond. Eliot Cutler, on the other hand, has responded. First, here is how I worded my question.

Mr. Cutler, I recently left a message on Libby Mitchell’s and Paul LePage’s respective Facebook pages asking them to either state or clarify their position on teaching creationism. Mitchell wants to be known as the “education governor”, so I presume she will favor teaching the basis of biology – evolution. (But I await… a response.) LePage, on the other hand, has had my question deleted and kicked me from his Facebook page. I presume he views his support for creationism as a liability.

What is your position? Thanks.

And once I write up a letter to the editor explain Paul LePage’s actions and inane, anti-science position, I hope his ignorance does become a liability. But first, here is Cutler’s response.

Hi Michael,

I support the teaching of evolution in elementary and secondary schools. Evolution is fundamental to every student’s comprehensive understanding of the world they live in and their ability to reason critically from evidence.

I have no objection to referencing creationism as an alternative view, but I do not believe it should be taught as part of the curriculum in public schools.

As a matter of principle, I do not believe that religion should make rules for government or that government should make rules for religion.

Eliot

It took me a second to digest this response. At first glance, being okay with references to creationism sounds sketchy, but then I thought back to my first biology course at university. Intelligent design and creationism were referenced before much got started. The professor basically covered his ground so that students wouldn’t be bringing silly challenges to him. He certainly welcomed a whole range of questions (and fielded them incredibly well, as he’s likely one of the smartest people I know), but he wasn’t there to undo 20 years of religious indoctrination. In that light, Cutler’s response works for me.

*Update: I’ve also asked Shawn Moody and Kevin Scott for their positions. They aren’t as high in the polling as the others, but they certainly aren’t off the radar.

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The basics

Posted on June 13, 2010 by Michael

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

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Evolutionary misfiring?

Posted on June 7, 2010 by Michael

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Microsatellites and mitochondria

Posted on March 24, 2010 by Michael

Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesn’t face problems such as recombination since it isn’t recombining with other DNA before being passed on (except through horizontal transfer, or “genetic swapping” between bacteria).

One recent discovery using mitochondrial DNA has found that a sort of “pre-human” was walking around while humans and Neanderthals were still rocking out.

The sequence indicates the hominin’s line diverged about a million years ago from the line that gave rise to both humans and Neanderthals and that split about 500,000 years ago.

That makes it younger than Homo erectus, the pre-human that spread out of Africa to much of the world about 1.9 million years ago.

“It is some new creature that has not been on our radar screen so far,” said Svaante Paabo, a colleague of Krause’s who specializes in analyzing ancient DNA.

And it would have lived near to both modern humans and Neanderthals. “There were at least three … different forms of humans in this area 40,000 years ago,” Paabo said.

The article goes on to state that more research is needed to determine just where it qualitatively sits on the evolutionary tree. My point, however, is that mtDNA has proved useful in this analysis, giving a tentative quantitative determination and a tentative qualitative indication.

This is all in stark contrast to microsatellites. These are short tandem repeats, or units of repeating DNA sequences. For example, CACACACACACACACACACA is commonly seen throughout eukaryotes and the chloroplastic genomes of plants (usually every few thousand base pairs). They are generally neutral.

Microsatellites have relatively high mutational rates for a variety of reasons. Whereas in mitochondria the mutational rate can partially be chalked up to the fact that mitochondria is bacterial in origin, microsatellites have polymerase slippage to thank, or bad DNA replication, let’s say. Other studies suggest unequal crossing-over. At any rate, this mutation rate lends itself to population studies using microsatellites.

By using microsatellites as genetic markers, it is possible to determine genetic variation within a population. This works for investigating both temporal and spatial population structure, two important factors in management and conservation of species. For instance, Lage et al. 2004 looked at Atlantic cod populations ranging across Browns Bank, Georges Bank, and Nantucket Shoals. At the time of the research, the Gulf of Maine cod were treated as a separate stock from the Nantucket Shoals and Georges Bank Atlantic cod. Browns Bank cod were even more separate as a stock since they are in Canadian waters. Using microsatellites, the researchers found Nantucket Shoals cod to have a distinct population structure from those on Georges Bank and Browns Bank, which were genetically similar. One likely reason is due to currents which keep Georges Bank cod on Georges Bank as well as somewhat rare currents which likely transport larvae from Browns Bank over the Fundian Channel (which adult cod are unlikely to traverse since they are ground-huggers and the channel is deep and cold). The conclusion is that the health of Atlantic cod populations might be better served by treating them as separate stocks based upon the discovered genetic variation, instead of the current method of utilizing particular geographical lines which may not reflect all population ‘barriers’.

The shortcoming, however, with microsatellites is that they are not useful for deep phylogenetic analysis. Their high mutation rate makes them virtually useless after a few thousand generations; they are good for pedigrees and population structure analysis, but they do not offer insights into distant relationships. Occasionally they may remain the same or nearly the same over long periods of time, but the rhyme and reason probably has nothing to do with the microsatellites themselves. Instead, they likely are located near a site of selection on a locus, thus conserving them for longer than just those few thousand generations.

Lage CR, Kuhn K, Kornfield I. (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fishery Bulletin, 102:289-297.

Update: Thanks to Chris Lage for offering his advice and corrections on this.

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Origins of vision

Posted on March 14, 2010 by Michael

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.”

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Neglected point

Posted on January 8, 2010 by Michael

One point I neglected about Tiktaalik is that its ability to walk on land was limited. Its limbs wouldn’t have been able to support it terribly well to do terribly much. Its life was likely spent more in the water than on land.

Coupled with the recent discovery of tetrapod footprints in a marine environment, the way to think of all this is that tetrapods did evolve at least 400 million years ago, but there were clearly still viable alternative lifestyles to go alongside fully terrestrial life (and still are). Nothing demands evolution be perfectly linear. (Neanderthals lived at the same time as our direct ancestors as recently as 30,000 years ago.) A further important fact is that while probably 90% or so of all fossils come from the ocean, they tend to be from the more settled sediments, i.e., not the shoreline, the evident habitat of these newly discovered tetrapods. That indicates a possible sampling bias. Just looking at Tiktaalik, it’s clear that its freshwater habitat lent itself to preserving fossils – aside from the area being targeted for its fossilizing properties, there were several examples extracted from the site.

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Tetrapods pushed back 18 million years

Posted on January 6, 2010 by Michael

The oldest tracks of four-legged animals have been discovered in Poland.

Rocks from a disused quarry record the “footprints” of unknown creatures that lived about 397 million years ago.

Scientists tell the journal Nature that the fossil trackways even retain the impressions left by the “toes” on the animals’ feet.

The team says the find means that land vertebrates appeared millions of years earlier than previously supposed.

This is especially interesting because Tiktaalik was discovered by Neil Shubin based upon a lack of land animals 390 million years ago but a prevalence 360 million years ago. He specifically looked for a place likely to have fossils that was 375 million years old in order to discover his transitional fossil. This new information doesn’t mean that he just got lucky – one would still expect to find transitional forms prior to true land animals – but a little luck was involved. (It was actually involved no matter what he wanted to find and when he wanted to find it because fossilization is so rare anyway.)

One important fact to note about Tiktaalik is that it likely lived in freshwater. This is key because a marine environment is less conducive to a full move onto land than a freshwater lake or river, and Tiktaalik shows evidence that it is closely related to later fully land animals. Think about it for a moment and it becomes obvious: you need to be able to drink freshwater, not salt water, in order to fully utilize the land. If your ancestors lived in freshwater, then the first transition has been made for you. That means the owners of these newly discovered footprints represent a transition of sorts, but they were still very much tied to a marine life, unlike Shubin’s discovery.

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Devil cancer update

Posted on January 3, 2010 by Michael

The devastating cancer spreading through the Tasmanian devil population has so far met resistance in at least one devil (Cedric), and possibly in his brother (Clinky).

Both were injected with dead tumours by scientists. Clinky produced no antibodies, but Cedric did and appears to have built-in defences against the mystery illness.

The experiments have now moved up a gear.

Researcher Alex Kriess says the pair have had live cancer cells inserted into their faces.

“They haven’t developed a tumour so far,” he said. “We injected very few cells so it might take a while until they develop anything that we can see.”

The next step is to see why Cedric may be resistant to the disease, which Jerry Coyne has deemed “can be regarded as a separate organism, genetically free to undergo independent evolution.” (The syntax is correct, but for clarity, it’s the disease that can be regarded as a separate organism.)

The most interesting aspect of all this is that Cedric comes from the side of the island not yet especially devastated by the disease. As more research is done, it will be interesting to find out if there is any sort of special history with cancer, even this specific cancer, that Cedric’s part of the island has had. That could be one driving cause behind the genetic difference to consider in addition to simple drift or geographical barriers.

Image via Jerry Coyne

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