Amy Maxmen - Evolution, You’re Drunk (Nautilus)

Amy Maxmen has an excellent article at Nautilus that kind of dispells the "myth" of evolution having an "imperative" toward increasing complexity.

The idea of directionality in nature, a gradient from simple to complex, began with the Greeks, who called nature physis, meaning growth. That idea subtly extended from changes over an organism’s lifetime, to changes over evolutionary time after Charles Darwin argued that all animals descend from a single common ancestor.

Being able to map the genomes of so many creatures has changed everything:

Biologists pushed aside trees based on how similar organisms looked to one another, and made new ones based on similarities in DNA and protein sequences. The results suggested that complex body parts evolved multiple times and had also been lost. One study found that winged stick insects evolved from wingless stick insects who had winged ancestors.[2] Another analysis suggested that extremely simple animals called acoel worms—a quarter inch long and with just one hole for eating and excreting—evolved from an ancestor with a separate mouth and anus.[3] Biologists’ arrow of time swung forward and backward and forward again.

Seems maybe evolution is less of "time's arrow" and more like "crooked lines."

Evolution, You’re Drunk

DNA studies topple the ladder of complexity

By Amy Maxmen | Illustration by Daniel Hertzberg
January 30, 2014

Amoebas are puny, stupid blobs, so scientists were surprised to learn that they contain 200 times more DNA than Einstein did. Because amoebas are made of just one cell, researchers assumed they would be simpler than humans genetically. Plus, amoebas date back farther in time than humans, and simplicity is considered an attribute of primitive beings. It just didn’t make sense.

The idea of directionality in nature, a gradient from simple to complex, began with the Greeks, who called nature physis, meaning growth. That idea subtly extended from changes over an organism’s lifetime, to changes over evolutionary time after Charles Darwin argued that all animals descend from a single common ancestor. When his contemporaries drew evolutionary trees of life, they assumed increasing complexity. Worms originated early in animal evolution. Creatures with more complex structures originated later. Biologists tweaked evolutionary trees over the following century, but generally, simple organisms continued to precede the complex.

Take the textbook scenario on early animal evolution. It essentially goes as follows: Single-celled organisms gained the ability to adhere to and communicate with one another more than 600 million years ago, and from the resulting colonies, the first multicellular animals emerged. Today’s sponges, sedentary animals on the sea floor with no guts, brains, or tissue layers, descend directly from some of these creatures. Some early animals then organized their cells into distinct tissue layers, and some of the cells formed nerve cells, muscle cells, and other types. Later yet, some animals developed serially repeated segments that served as a platform for legs and claws in their descendants. Then an animal with a spinal column evolved, and then one with a column surrounded by bony vertebrae. A recent branch to split from the tree blossomed into humans.

Scientists’ belief in this scenario has remained relatively unchanged for a century. It reflects the growth we observe during an organism’s development, and it’s been tracked over evolutionary time, too. Paleontologists have found fossils to support this arrangement, and they’ve also quantified increasing complexity within animal lineages. For example, an analysis of the waves, or sutures, in shells of extinct mollusks called ammonoids—snail-like sisters to nautiluses—shows that their designs became eight times as complex over 108 million years.[1]


The waves, or sutures, in the shells of one group of ammonoids became eight times more complex over 108 million years.Maureen Griswold | Source: Paleobiology (See Reference 1 below.)
Before the advent of rapid, accurate, and inexpensive DNA sequencing technology in the early 2000s, biologists guessed that genes would provide more evidence for increasing complexity in evolution. Simple, early organisms would have fewer genes than complex ones, they predicted, just as a blueprint of Dorothy’s cottage in Kansas would be less complicated than one for the Emerald City. Instead, their assumptions of increasing complexity began to fall apart. First to go was an easy definition of how complexity manifested itself. After all, amoebas had huge genomes. Now, DNA analyses are rearranging evolutionary trees, suggesting that the arrow scientists envisioned between simplicity and complexity actually spins like a weather vane caught in a tornado.

AFTER GENOME SIZES failed to fit notions of simplicity and complexity, researchers hypothesized that gene number—genes being the sections of the genome that encode proteins—might instead reflect them. For a few years, that seemed about right. Humans have about 22,000 genes while the mosquito Anopheles gambiae has about 14,000. Then, in 2007, an international team of researchers sequenced the genome of the plant-like sea anemones, marine creatures that lack muscles, heads, rear-ends, and brains. To their surprise, anemones had more genes than insects, including some genes that humans possess but flies do not. Even more perplexing: Sea anemones evolved before flies and humans, some 560 million years ago. That meant animals might have been genetically complex from the start. “When I was younger, and we knew less, we thought that organisms gained genes over millions of years and that the earliest animals were genetically very simple,” says Bill Pearson, a computational biologist at the University of Virginia who developed some of the first techniques to compare protein sequences among organisms. “We think that less now,” he adds.

Then molecular analyses did something else. They rearranged the order of branches on evolutionary trees. Biologists pushed aside trees based on how similar organisms looked to one another, and made new ones based on similarities in DNA and protein sequences. The results suggested that complex body parts evolved multiple times and had also been lost. One study found that winged stick insects evolved from wingless stick insects who had winged ancestors.[2] Another analysis suggested that extremely simple animals called acoel worms—a quarter inch long and with just one hole for eating and excreting—evolved from an ancestor with a separate mouth and anus.[3] Biologists’ arrow of time swung forward and backward and forward again.

Late last year, the animal evolutionary tree quaked at its root. A team led by Joseph Ryan, an evolutionary biologist who splits his time between the National Genome Research Institute in Bethesda, Md. and the Sars International Center for Marine Molecular Biology in Bergen, Norway, analyzed the genome from a comb jelly, Mnemiopsis leidyi, a complex marine predator with muscles, nerves, a rudimentary brain, and bioluminescence, and found that the animals may have originated before simple sponges, which lack all of those features.[4]


The comb jelly, Mnemiopsis leidyi, snags prey with its mucus-covered lobes. An analysis of its genome suggests the group might have evolved before all other living animals.William Browne, University of Miami
If comb jellies evolved before sponges, the sponges might have lost the complexity that the ancestor uniting them and comb jellies possessed. Or, that ancestor—the ancestor of all living animals—had the genes to build brains and muscles, but did not form those parts, and neither did sponges. If this is true, then comb jellies deployed the genome they inherited to build a brain, nervous system, and muscles, independent of other animals. There’s some support for this possibility: A unique set of genes seems to underlie comb jellies’ muscles.

Both hypotheses run counter to scenarios in which organisms evolve to be increasingly complex. In one, a complex nervous system and muscles were lost in the sponges. In the other, the sponges had the genetic capability for complex features but stayed simple, while a more primitive group, the comb jellies, acquired brains and muscles that help them chase down prey. Furthermore, the idea that complex parts like a brain and nervous system—including nerve cells, synapses, and neurotransmitter molecules—could evolve separately multiple times perplexes evolutionary biologists because parts are gained one at a time. The chance of the same progression happening twice in separate lineages seems unlikely—or so biologists thought. “Traditional views are based on our dependence on our nervous system,” says Ryan. “We think the nervous system is the greatest thing in the world so how could anything lose it,” he says. “Or, it’s the greatest thing in the world, so how could it happen twice.”

WITH COMB JELLIES at the base of the tree, evolution suddenly seems less like a march towards complexity and more like a meandering stroll. This isn’t a new idea. Back in 1996, evolutionary biologist Stephen Jay Gould posited that evolution progresses like a drunkard’s walk. Organisms, he said, stand an equal chance of becoming simpler or more complex over millions of years—although sometimes there’s a lower limit on how simple they can possibly be, just as a drunk may fall into a gutter at the far left side of the road. An Internet meme even celebrates oddities that result from evolution’s stumble: “Go Home Evolution, You’re Drunk,” features organisms with sub-optimal traits that have managed to survive just fine.

It’s mutations that cause body parts to become simpler or more complex, so to see whether they naturally cause one state more often than the other, Jukka Jernvall, an evolutionary biologist at the University of Helsinki in Finland, experimented with teeth. According to the fossil record, mammals’ teeth went from tiny, pointy daggers 200 million years ago to more complex shapes with bumps and grooves. “For the first half of [mammals’] existence, teeth were pretty simple,” Jernvall says. “Then they went wild.”

Jernvall’s team induced mutations in genes involved in tooth formation in mice, and found that most of the mutations caused teeth to become simpler than they usually are.[5] To form a more complex tooth, the team had to induce multiple molecular changes at once. The results suggest that reductions in complexity should evolve more easily than increases in complexity. Without pressure from the environment, teeth would have stayed simple. The fact that they did not means mammals with complex teeth were at a sizable advantage. Jernvall speculates that these mammals feasted on flowering plants that their pointy-toothed sisters could not grind. “Tooth complexity was ecologically driven through diet,” he says.

Jernvall’s study shows how complexity in tooth shape can evolve, but it does not speak to other trends in mammalian features, such as their number of vertebrae, changes in intelligence, or their number of genes. The sheer number of features for any given organism makes complexity an ineffable trait to grasp, says Dan McShea, an evolutionary biologist at Duke University in Durham, N.C. Shell designs and tooth bumps aren’t inherently perfect reflections of complexity, they’re just amenable to study. Furthermore, he says, people often choose to define complexity by what puts humans on top. If complexity were instead defined by features that allow an organism to survive successfully, he says cyanobacteria might be at the pinnacle level, because they have flourished for 3.5 billion years while many lineages of mammals have gone extinct within a fraction of that time. McShea warns, “This impression of directionality may be an illusion.”

Perhaps the fact that people are stunned whenever organisms become simpler says more about how the human mind organizes the world than about evolutionary processes. People are more comfortable envisioning increasing complexity through time instead of reversals or stasis. Physicist Sean Carroll calls humans “terrible temporal chauvinists” for this reason, because they desperately want the street from the past to the future to run in one direction. The textbook scenarios on early animal evolution might be correct, but they should be treated as hypotheses built by temporal chauvinists. When new data suggests a rearrangement, it must be considered no matter how perplexing the conclusion seems.

Casey Dunn, an evolutionary biologist at Brown University in Providence, R.I. who took part in the still-contentious comb jelly project, now doubts all notions of increasing complexity. Instead, he says the environment selects whatever form handles the challenges at hand, be it simple, complex, or plain ugly. Mother Nature, with her 4 billion years of experience, does not work like Steve Jobs, continuously designing sleeker versions. When asked whether de-evolution, a reversal from the complex to the simple, happens frequently, Dunn replies, sure. “But,” he adds, “I wouldn’t call that de-evolution, I’d call it evolution.”

References

1. Saunders, W. B. & Work, D. M. Evolution of Shell Morphology and Suture Complexity in Paleozoic Prolecanitids, the Rootstock of Mesozoic Ammonoids. Paleobiology 23, 301-325 (1997).
2. Whiting, M. F., Bradler, S. & Maxwell, T. Loss and recovery of wings in stick insects. Nature 421, 264-267 (2003).
3. Philippe, H., et al. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470, 255-258 (2011).
4. Ryan, J., et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342 (2013).
5. Harjunmaa, E., Kallonen, A., Voutilainen, M., Hamalainen, K., Mikkola, M. L., & Jernvall, J. On the difficulty of increasing dental complexity. Nature 483, 324-327 (2012).

Human Genetics Are Not Uniform Even within the Same Person

For as long as I can remember, the consensus was that it is rare for the cells in a single healthy person to differ genetically in a significant way. Not so much. Now, scientists see individuals with multiple genomes much more frequently. "Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people."

Where was this science when cyclist Tyler Hamilton was defending himself against blood doping allegations with the claim that he had chimerism?

But seriously, this is an excellent article from Carl Zimmer at The New York Times.

DNA Double Take

By CARL ZIMMER
Published: September 16, 2013 


DNA sequencing elements displayed on a monitor. Noah Berger for The New York Times.
From biology class to “C.S.I.,” we are told again and again that our genome is at the heart of our identity. Read the sequences in the chromosomes of a single cell, and learn everything about a person’s genetic information — or, as 23andme, a prominent genetic testing company, says on its Web site, “The more you know about your DNA, the more you know about yourself.”

 

A DNA sample. Sequencing has become faster and relatively cheaper in the last 20 years.

But scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people.

“There have been whispers in the matrix about this for years, even decades, but only in a very hypothetical sense,” said Alexander Urban, a geneticist at Stanford University. Even three years ago, suggesting that there was widespread genetic variation in a single body would have been met with skepticism, he said. “You would have just run against the wall.”

But a series of recent papers by Dr. Urban and others has demonstrated that those whispers were not just hypothetical. The variation in the genomes found in a single person is too large to be ignored. “We now know it’s there,” Dr. Urban said. “Now we’re mapping this new continent.”

Dr. James R. Lupski, a leading expert on the human genome at Baylor College of Medicine, wrote in a recent review in the journal Science that the existence of multiple genomes in an individual could have a tremendous impact on the practice of medicine. “It’s changed the way I think,” he said in an interview.

Scientists are finding links from multiple genomes to certain rare diseases, and now they’re beginning to investigate genetic variations to shed light on more common disorders.

Science’s changing view is also raising questions about how forensic scientists should use DNA evidence to identify people. It’s also posing challenges for genetic counselors, who can’t assume that the genetic information from one cell can tell them about the DNA throughout a person’s body.

Human Blueprint

When an egg and sperm combine their DNA, the genome they produce contains all the necessary information for building a new human. As the egg divides to form an embryo, it produces new copies of that original genome.

For decades, geneticists have explored how an embryo can use the instructions in a single genome to develop muscles, nerves and the many other parts of the human body. They also use sequencing to understand genetic variations that can raise the risk of certain diseases. Genetic counselors can look at the results of genetic screenings to help patients and their families cope with these diseases — altering their diet, for example, if they lack a gene for a crucial enzyme.

The cost of sequencing an entire genome has fallen so drastically in the past 20 years — now a few thousand dollars, down from an estimated $3 billion for the public-private partnership that sequenced the first human genome — that doctors are beginning to sequence the entire genomes of some patients. (Sequencing can be done in as little as 50 hours.) And they’re identifying links between mutations and diseases that have never been seen before.

Yet all these powerful tests are based on the assumption that, inside our body, a genome is a genome is a genome. Scientists believed that they could look at the genome from cells taken in a cheek swab and be able to learn about the genomes of cells in the brain or the liver or anywhere else in the body.

In the mid-1900s, scientists began to get clues that this was not always true. In 1953, for example, a British woman donated a pint of blood. It turned out that some of her blood was Type O and some was Type A. The scientists who studied her concluded that she had acquired some of her blood from her twin brother in the womb, including his genomes in his blood cells.

Chimerism, as such conditions came to be known, seemed for many years to be a rarity. But “it can be commoner than we realized,” said Dr. Linda Randolph, a pediatrician at Children’s Hospital in Los Angeles who is an author of a review of chimerism published in The American Journal of Medical Genetics in July.

Twins can end up with a mixed supply of blood when they get nutrients in the womb through the same set of blood vessels. In other cases, two fertilized eggs may fuse together. These so-called embryonic chimeras may go through life blissfully unaware of their origins.

One woman discovered she was a chimera as late as age 52. In need of a kidney transplant, she was tested so that she might find a match. The results indicated that she was not the mother of two of her three biological children. It turned out that she had originated from two genomes. One genome gave rise to her blood and some of her eggs; other eggs carried a separate genome.

Women can also gain genomes from their children. After a baby is born, it may leave some fetal cells behind in its mother’s body, where they can travel to different organs and be absorbed into those tissues. “It’s pretty likely that any woman who has been pregnant is a chimera,” Dr. Randolph said.

Everywhere You Look

As scientists begin to search for chimeras systematically — rather than waiting for them to turn up in puzzling medical tests — they’re finding them in a remarkably high fraction of people. In 2012, Canadian scientists performed autopsies on the brains of 59 women. They found neurons with Y chromosomes in 63 percent of them. The neurons likely developed from cells originating in their sons.

In The International Journal of Cancer in August, Eugen Dhimolea of the Dana-Farber Cancer Institute in Boston and colleagues reported that male cells can also infiltrate breast tissue. When they looked for Y chromosomes in samples of breast tissue, they found it in 56 percent of the women they investigated.

A century ago, geneticists discovered one way in which people might acquire new genomes. They were studying “mosaic animals,” rare creatures with oddly-colored patches of fur. The animals didn’t inherit the genes for these patches from their parents. Instead, while embryos, they acquired a mutation in a skin cell that divided to produce a colored patch.

Mosaicism, as this condition came to be known, was difficult to study in humans before the age of DNA sequencing. Scientists could only discover instances in which the mutations and the effects were big.

In 1960, researchers found that a form of leukemia is a result of mosaicism. A blood cell spontaneously mutates as it divides, moving a big chunk of one chromosome to another.

Later studies added support to the idea that cancer is a result of mutations in specific cells. But scientists had little idea of how common cases of mosaicism were beyond cancer.

“We didn’t have the technology to systematically think about them,” said Dr. Christopher Walsh, a geneticist at Children’s Hospital in Boston who recently published a review on mosaicism and disease in Science. “Now we’re in the midst of a revolution.”

Benign Differences

The latest findings make it clear that mosaicism is quite common — even in healthy cells.

Dr. Urban and his colleagues, for example, investigated mutations in cells called fibroblasts, which are found in connective tissue. They searched in particular for cases in which a segment of DNA was accidentally duplicated or deleted. As they reported last year, 30 percent of the fibroblasts carried at least one such mutation.

Michael Snyder of Stanford University and his colleagues searched for mosaicism by performing autopsies on six people who had died of causes other than cancer. In five of the six people they autopsied, the scientists reported last October, they found cells in different organs with stretches of DNA that had accidentally been duplicated or deleted.

Now that scientists are beginning to appreciate how common chimerism and mosaicism are, they’re investigating the effects of these conditions on our health. “That’s still open really, because these are still early days,” Dr. Urban said.

Nevertheless, said Dr. Walsh, “it’s safe to say that a large proportion of those mutations will be benign.” Recent studies on chimeras suggest that these extra genomes can even be beneficial. Chimeric cells from fetuses appear to seek out damaged tissue and help heal it, for example.

But scientists are also starting to find cases in which mutations in specific cells help give rise to diseases other than cancer. Dr. Walsh, for example, studies a childhood disorder of the brain called hemimegalencephaly, in which one side of the brain grows larger than the other, leading to devastating seizures.

“The kids have no chance for a normal life without desperate surgery to take out half of their brain,” he said.

Dr. Walsh has studied the genomes of neurons removed during those surgeries. He and his colleagues discovered that some neurons in the overgrown hemisphere have mutations to one gene. Two other teams of scientists have identified mutations on other genes, all of which help to control the growth of neurons. “We can get our hands on the mechanism of the disease,” said Dr. Walsh.

Other researchers are now investigating whether mosaicism is a factor in more common diseases, like schizophrenia. “This will play itself out over the next 5 or 10 years,” said Dr. Urban, who with his colleagues is studying it.

Moving Cautiously

Medical researchers aren’t the only scientists interested in our multitudes of personal genomes. So are forensic scientists. When they attempt to identify criminals or murder victims by matching DNA, they want to avoid being misled by the variety of genomes inside a single person.

Last year, for example, forensic scientists at the Washington State Patrol Crime Laboratory Division described how a saliva sample and a sperm sample from the same suspect in a sexual assault case didn’t match.

Bone marrow transplants can also confound forensic scientists. Researchers at Innsbruck Medical University in Austria took cheek swabs from 77 people who had received transplants up to nine years earlier. In 74 percent of the samples, they found a mix of genomes — both their own and those from the marrow donors, the scientists reported this year. The transplanted stem cells hadn’t just replaced blood cells, but had also become cells lining the cheek.

While the risk of confusion is real, it is manageable, experts said. “This should not be much of a concern for forensics,” said Manfred Kayser, a professor of Forensic Molecular Biology at Erasmus University in Rotterdam. In the cases where mosaicism or chimerism causes confusion, forensic scientists can clear it up by other means. In the Austrian study, for example, the scientists found no marrow donor genomes in the hair of the recipients.

For genetic counselors helping clients make sense of DNA tests, our many genomes pose more serious challenges. A DNA test that uses blood cells may miss disease-causing mutations in the cells of other organs. “We can’t tell you what else is going on,” said Nancy B. Spinner, a geneticist at the University of Pennsylvania, who published a review about the implications of mosaicism for genetic counseling in the May issue of Nature Reviews Genetics.

That may change as scientists develop more powerful ways to investigate our different genomes and learn more about their links to diseases. “It’s not tomorrow that you’re going to walk into your doctor’s office and they’re going to think this way,” said Dr. Lupski. “It’s going to take time.”


~ A version of this article appears in print on September 17, 2013, on page D1 of the New York edition with the headline: DNA Double Take.