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Thursday, September 27, 2012

Endogenous Retroviruses are without a doubt one of the coolest phenomena in all of biology. The human genome is made up of a string of some 3 billion "letters" (either A,T,C or G) using the alphabet of DNA. However, a significant portion of that string of letters (~8%) is not actually human DNA. Instead, it is composed of strands of virus DNA (chunks around 10,000 letters long) that have inserted themselves into our genome. How does this happen, and is there anything we can learn from it?

As you may have learned in high school biology, viruses are so effective because they hijack our own cellular machinery to spread themselves. A virus can be as simple as a strand of DNA or RNA (with a protective coat of protein) that contains the instructions for copying and making more of itself. When this virus gets inside one of your cells, your cell can't tell the difference between your genetic material and the viral genetic material. So your cellular machinery starts reading the viral DNA/RNA and follows the instructions. Unfortunately, instead of instructions that tell the cell to make more healthy human proteins, the instructions tell the cell to make more virus! Thousands of brand new viruses then exit that cell, proceed to infect other cells, and begin a chain reaction that can make you ill or worse as more and more cells get infected.

Sometimes the short strand of viral DNA floats around inside the nucleus of a cell on it's own, but sometimes it actually inserts itself into the massive length of letters that is human DNA (Only one specific type of virus does this: retroviruses, of which HIV is the most well-known example).

Retroviral DNA Insertion

Every once and a while, a combination of three rare events occurs in a retroviral infection:

1) The virus happens to affect a germ cell (either a sperm or an egg)
2) The virus inserts itself into the germ cell DNA without seriously harming the cell or the organism
3) An infected sperm or egg cell happens to be the one that combines with it's complimentary partner during sexual reproduction, creating a new organism.

When an individual is born from a cell infected with a retrovirus, that genetic material will be imbedded in all of his or her cells. It will actually have become part of the individual's genome. (This usually only happens when the virus is no longer infective for one or more reasons. Otherwise the germ cell or offspring organism would probably not survive!).

Finally, one more rare event has to occur for the retrovirus to move from being part of the genome of an individual to being part of the genome of a population:

4) The infected individual has to get lucky enough to pass his or her copy
of the now "Endogenous" RetroVirus [ERV] to its descendants, and
eventually throughout the entire population of the species.

Retroviral infections occur all the time. However, for all 4 of the above
situations to occur, it takes an extremely lucky chance. Even in a population
of millions or billions of individuals, it can take thousands of
years for a single retrovirus to become endogenous to a species. But guess
what? Life has been evolving for billions of years. Our DNA is absolutely riddled
with ERVs.

This gives us a great chance to confirm the phylogenic tree of life
that people have been working on for centuries. Previously, people had to guess
which animals were more closely related to other animals by comparing their how similar they look. For example, we had a pretty good idea that chimps are
more closely related to gorillas than they are to spider monkeys, because they look
more closely related. Now, we can prove it with ERVs (We can prove it with lots of
other genetic evidence as well, but ERVs are one of the coolest and most
straightforward ways).

Imagine that a common ancestor of humans and chimpanzees was infected by an
endogenous retrovirus. Over 6 million years, humans diverged from the chimpanzees, but
the short (10,000 "letter" long strand of DNA) ERV is still unmistakable in my genome, your genome, and
the genome of all chimpanzees, in precisely the same location.If
not for the bold statement, one could easily argue that chimpanzees don't actually share an ancestor with us:

"Couldn't
chimpanzees and humans both have been separately infected by the same retrovirus?"

Sure, but the ERV in chimps wouldn't happen to have been randomly inserted between the
exact same two letters in as the ERV in humans' 3 billion-letter genome, which is what we observe.

We don't have to be hypothetical about all of this. As it turns out,
this exact scenario has happened tens of thousands of times. Most of that 8% of
our genome made up of ERVs is shared with chimpanzees. There are of course a
few ERVs that were inserted after our divergence with chimps, as would
be expected, but that didn't happen too long ago in the geologic time scale.

Young Chimpanzees. Attribution : Delphine Bruyere, CC License

Humans and chimps share many ERVs. Gorillas also share many ERVs with us (see ERV1 in the following diagram),
but slightly fewer than between chimps and us, because Gorillas diverged from our ancestors before chimps
did. Humans and chimps shared the same
common ancestors for a couple million more years, providing time for additional
retroviral insertions that are now shared by both species (See ERV2 in the
following diagram).

Hypothetical ERV Insertion in Great Apes

If the theory of evolution were a good theory, it would make testable
predictions. A testable prediction of the theory of evolution would look
something like this:

All ERVs that chimps share (in the same genetic location) with gorillas will also be
shared with humans.

We can make such a claim because if a gorilla and chimp share an ERV (Like
ERV1, the red ERV in the diagram above), it would have been acquired earlier
than 8 million years ago by a common ancestor of chimps and gorillas. Since
humans share the same common ancestor with gorillas that chimps do,humans
should also share the same ERV. Of course, we now have the technology to test
this prediction, and find it to be nearly always true. In fact, we can show the
same thing with all sorts of organisms! House cats and tigers share tons of ERVs,
many of which are not shared by humans, because they diverged from our lineage
so long ago. However, any ERV that housecats share with humans will also be found
in tigers!

I find ERVs fascinating not only because of the unique mechanism by which
they become a part of us, but also because of the great confirmation
they give us of the theory of evolution. There is simply no other explanation
for the perfect pattern we see: closely related animals share a huge number of
ERVs, while more distant cousins share fewer, and distant cousins never share
ERVs in the same location that the closer cousins do not.

This
is intended to be a high-level introduction to ERVs. A more thorough discussion
would include an analysis of things like insertion locus specificity, excision
of ERVs, ERVs acting as promoter regions or with other functionality, latent infectivity, etc. At
this point I will leave it up to the reader to learn more about that elsewhere.

Sunday, September 9, 2012

I don't watch TV, so it is understandable that I would miss such things. However, in the past few months, two people have mentioned a mockumentary to me called Mermaid: The Body Found,in whichmultiple "scientists" claim to have discovered a myriad of evidence for the existence of mermaids. First of all, one of the two people mentioning it could actually not distinguish it from a real documentary. This brings all sorts of things to my mind (how do we educate children to think critically? What are the ethical issues around producing television shows/movies that are fictional but might be mistaken for truth by uneducated viewers?). Second of all, the show makes all sorts of references to science and scientific theories that are bogus. Lots of movies like to use fictional "scientific" mumbo jumbo to sound more legitimate to the average audience member, and I do not spend much time poking holes in or debunking those. However, since I personally know at least one person who was actually convinced that mermaids are fucking real by this show, it might be worth my time (and judging by the youtube comments, on the video, other people were fooled as well). It will at least be entertaining for me.

How do we know it is fake?
I am not going to spend much time here unless I am specifically asked.

So much of the science in the films is obviously bogus to anyone with any college degree in a science related field. Read on.

Some scientific inaccuracies in the film

The film claims that the hypothetical mermaids are responsible for a sound of unknown origin dubbed "The Bloop" recorded by underwater hydrophones in 1997. This noise was transmitted through over 3,000 miles of ocean, at a frequency of 10-40 Hz. To create a deep noise this loud, an organism would need to be multiple times larger than the largest blue whale. Yet at the same time, the film claims that some of the recordings contained audio signatures at such a high frequency that they were "outside the range of human hearing" and had to be slowed down. So which is it? Are these mermaids giant sea monsters dwarfing whales and dinosaurs? Or tiny water mammals capable of producing bat-like high frequency sounds (that, by the way, would not be able to travel any significant distance under water)

Snap zooming of the lens of what purports to be a cell phone video camera in 2004. (Two boys who stumble upon a mermaid body washed ashore)

Mumbo Jumbo by a linguistics guy about identification of signifiers (words) in a recording of the mermaids. Somehow, based on a recording, with no observation of the behavior of the organism, he could "crack the code" and identify hundreds of words.

"Dr. Visser" says things no biologist with any understanding of the evolution of the great apes would say. "A new species of Hominid... these are humans, and our closest relatives". Yet they claim to have diverged with our ancestors 6 million years ago. So what about all of these species which would be closer relatives? These mermaids would certainly not be a member of the genus homo (the first appearing ~2 million years ago), and therefore would certainly not be classified has humans.

"Blubber had a unique fatty acid that could remain liquid and insulate well in cold water" <- scientifically meaningless. Hundreds of fatty acids fit this description. If you have "never seen anything like that before," you are not a scientist.

You found a blood protein called myoglobin in the mermaid remains? Too bad every single other vertebrate has the same protein, including us. Completely irrelevant, but sounds sciency.

The mermaid remains had a "network of blood vessels that supply heat to critical organ systems." Isn't that what all networks of blood vessels do?

"Like other marine mammals, we have an insulating layer of fat", yeah, and like other NON-marine mammals too.

The potential for mermaids to have evolved

The film displays a misunderstanding of the "aquatic ape" hypothesis (A hypothesis for which there is no scientific evidence, stating that the ancestors of humans spent a few million years adapting for an aquatic environment, resulting in things like hairlessness). The film twists this theory to one that states that it was not our ancestors that adapted to an aquatic environment, but our cousins (having diverged from our line before adapting the aquatic environment). See images below.

The aquatic ape hypothesis

What the film claims

The film uses polar bears as an example of an animal that has evolved aquatic adaptations in support of the possibility that human ancestors could do the same. However modern polar bears diverged from modern brown bears 4-5 million years ago, not 125,000 years ago. And 4 million years is so little time evolutionarily that polar bears and brown bears can still mate and produce fertile offspring. Yet they claim the mermaids diverged from humans only 5-6 million years ago?

All whales, dolphins, and porpoises share a single common ancestor among land animals. The film claims that this ancestor was related to the wolf (based on teeth similarities), but genetic evidence over the past couple decades shows that they are much more closely related to hippopotamuses .

It took some 50 million years for whales to evolve from land mammals to their current state. See this article for more information. The evolution of an ape to a mermaid is probably equally drastic.

The flipper of the mermaid is shown evolving by a fusing of the legs. This strikes me as an unlikely way for a flipper to evolve. The flippers of whales evolved from a tail. Early whales had legs AND a flipper, and in fact, many modern whales still have vestigial leg bones.

That's about all I have time for tonight. I won't say it would be impossible for such creatures to evolve from apes, I think that would be a very drastic change over a relatively short time. I think it deserves about as much thought as a hypothesis saying "What if one of the ancestors of horses diverged and grew a horn!! It would be like a unicorn!" or "What if one of the ancestors of humans diverged and got really small and developed an Irish accent, and became leprechauns!" without any evidence whatsoever supporting their claim.

Although it was an interesting film, I highly dislike it due to its potential to mislead people and confuse them about real science.