Tuesday, May 5, 2015

Scientists probe DNA for clues on modification

One recurring theme in reader questions, especially from creationists, is that Darwinian evolution can't explain big changes - the invention of fur or feathers, kidneys or brains. These readers don't see how such innovation could possibly come about through random spelling errors in DNA, no matter how many millions of years they had to accumulate.

Scientists probe DNA for clues on modification

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One recurring theme in reader questions, especially from creationists, is that Darwinian evolution can't explain big changes - the invention of fur or feathers, kidneys or brains. These readers don't see how such innovation could possibly come about through random spelling errors in DNA, no matter how many millions of years they had to accumulate.

". . . the concept of 'descent with modification' cannot generate more complex systems . . . the old adage that if you give 1,000 monkeys 1,000 years to randomly type we could get the works of Shakespeare is false. It is not mathematically possible. We would simply get 1,000 years of gibberish," wrote one reader.

A similar complaint can be seen on creationist websites such as Answersingenesis: "Mutations are just 'typographic errors' that occur as genetic script is copied. Mutations have no ability to compose genetic sentences, and thus no ability to make evolution happen at all."

These statements ignore the ordering power of natural selection and the fact that variation comes from sources beyond simple typos.

While some look for answers in Genesis, Yale biologists Gunter Wagner and Vincent Lynch are looking in DNA. There, they have found what may be a genetic underpinning of one of the most striking leaps in our own evolutionary journey - the invention of pregnancy.

The key to this change, by which placental mammals emerged, was not a random spelling error. Instead, a whole swath of DNA apparently invaded our mammalian ancestors' genomes 100 million years ago and copied itself thousands of times. Where this invader came from is still debated.

This is just the latest example of something biologists have known for a while: Evolution doesn't work like monkeys at typewriters. Variation is essential for natural selection to operate, but the way variety is generated in DNA is more like a pack of monkeys using the MacBook Pro, cutting and pasting and stealing from one another like shameless plagiarists.

There are many ways that whole chunks of genetic code can be rearranged, moved, turned around, copied and pasted, and otherwise altered.

Organisms can also steal from one another, as monkeys with computers could plagiarize one another's text through the World Wide Web. But in life, the pool of genetic information is also interconnected in ways science is just beginning to understand.

Viruses, for example, allow DNA to move between different species. They may account for the origin of some of what scientists call parasitic DNA - strings of code that appear to have invaded our chromosomes and started copying themselves.

Some of this parasitic stuff takes the form of defunct viruses that get stuck inside our cells. About eight percent of our DNA is made of these so-called endogenous retroviruses, which used to be able to incorporate their genetic code into those of their hosts, but somewhere along the line lost the ability to get out of our cells and infect others.

About 40 percent of our DNA comes from another type of genetic parasites called "transposable elements." These are pieces of DNA that can copy themselves within our own genetic codes, sometimes thousands of times. Their origin is murkier, but some think viruses transfer them between species.

Some parasitic DNA might have been harmful initially. In other cases, it triggered change that offered some advantage.

That's what may have happened with the origin of pregnancy, said Wagner, whose latest findings were published in Nature Genetics. That's noteworthy because it addresses the invention of a new type of cell, said Swarthmore College biologist Scott Gilbert.

New species can arise by changing the way existing genes are turned on and off in different parts of the body, he said. A turtle, for example, repurposes bone cells to make a shell. "But the origin of a new cell type, a much rarer occurrence, makes possible a new mode of existence," he said.

Mammalian pregnancy is such a new mode of existence. Until about 100 million years ago, mammals either laid eggs, as the platypus does today, or had a more superficial pregnancy, in which the fetus does into invade the tissue of the mother. But once complete mammalian pregnacy emerged, it floursihed. Today there are more than 5,000 species of placental mammals and only 300 marsupials.

To seek out the genetic changes behind this leap, Wagner studied tissue from the uterus of a marsupial, the opossum, and compared it with that from a human, a dog, and an armadillo. He chose the armadillo because it is the placental mammal most distantly related to humans, he said, which means any traits we share with them are likely to be shared across all placental mammals.

What he found was that we placental mammals all have thousands of copies of a stretch of DNA called MER20, which is absent in the opossum. And these MER20 elements apparently activate a whole slew of genes in uterine tissue.

Once the MER20 elements got into an early mammal's DNA, they copied themselves thousands of times. We humans have 20,000 of them. "This was a brutal invasion of the genome," said biologist Cedric Feschotte of the University of Texas, Arlington.

That doesn't prove that this particular transposable element led to the invention of the placenta, but it may have contributed something, Feschotte said. Where these invaders came from is an open question, he said. "It almost looks like they appeared by magic." He thinks they came from some other species, picked up and transferred by an ancient viral infection.

Viruses are good at cutting and pasting DNA, and are capable of picking up DNA from one animal and incorporating it into the genetic code of another species. If such a virus gets into an animal's egg or sperm cells, it can be carried into future generations.

Feschotte says a number of animals appear to carry DNA that has crossed species lines. He calls these segments "space invaders" and has found them in rats, mice, bats, bushbabies, frogs, lizards, and an elephant relative called a tenrec.

Some of these invaders may have triggered changes that improved their recipients' fitness relative to competitors'. That's where natural selection comes in, favoring the variants best able to survive and reproduce.

Darwin didn't have the benefit of modern genetics, but now that we do, it's clear natural selection had a lot more to work with than the plunking of monkeys at typewriters.

 


Contact staff writer Faye Flam at 215-854-4977 or fflam@phillynews.com. Read her "Planet of the Apes" blog at www.philly.com/evolution.

 

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