3. The Origin of Species

Archive of Past Articles for Chapter 3

2009 September 7. Where Did All the Flowers Come From? By Carl Zimmer, The NY Times. Excerpt: Throughout his life, Charles Darwin surrounded himself with flowers. ...But despite his intimate familiarity with flowers, Darwin once wrote that their evolution was “an abominable mystery.”
...The fossil record...offered Darwin little enlightenment about the early evolution of flowers. At the time, the oldest fossils of flowering plants came from rocks that had formed from 100 million to 66 million years ago during the Cretaceous period. Paleontologists found a diversity of forms, not a few primitive forerunners.
Long after Darwin’s death in 1882, the history of flowers continued to vex scientists. But talk to experts today, and there is a note of guarded optimism....
The discovery of new fossils is one source of that new excitement. But scientists are also finding a wealth of clues in living flowers and their genes. They are teasing apart the recipes encoded in plant DNA for building different kinds of flowers. Their research indicates that flowers evolved into their marvelous diversity in much the same way as eyes and limbs have: through the recycling of old genes for new jobs....

2009 February 9. On Darwin’s ‘On the Origin of Species’. The NY Times. In addition to being the 200th anniversary of Darwin's birth, 2009 is the 150th anniversary of the publication of his fundamental work, "On the Origin of Species." As with many original sources, it is known mostly by reputation. Few people who are not biologists read Darwin in the original. But his writing can still offer surprises, insights and pleasures, and it can be sampled here, with selections by prominent scientists of their favorite passages and discussions of why these passages are important....

2009 February 9. Darwin, Ahead of His Time, Is Still Influential. By Nicholas Wade, The New York Times. Excerpt: Darwin’s theory of evolution has become the bedrock of modern biology. But for most of the theory’s existence since 1859, even biologists have ignored or vigorously opposed it, in whole or in part.
It is a testament to Darwin’s extraordinary insight that it took almost a century for biologists to understand the essential correctness of his views.
Biologists quickly accepted the idea of evolution, but for decades they rejected natural selection, the mechanism Darwin proposed for the evolutionary process....
And biologists are still arguing about group-level selection, the idea that natural selection can operate at the level of groups as well as on individuals....
It is somewhat remarkable that a man who died in 1882 should still be influencing discussion among biologists....

2009 February 9. Genes Offer New Clues in Old Debate on Species’ Origins. By CAROL KAESUK YOON, The New York Times. Excerpt: Charles Darwin called it the “mystery of mysteries,” a problem so significant and one he was so sure he had solved that he named his world-changing work after it: “On the Origin of Species.” So he might be surprised to learn that 150 years after the publication of his book, the study of how species originate, a process known as speciation, is not only one of the field’s most active areas of study, but also one of its most contentious....
...“A decade ago, the joke was that spell-checkers regularly attempted to substitute the word ‘speciation’ with ‘speculation,’” Mohamed Noor, an evolutionary biologist at Duke University, wrote in a commentary in the journal Nature. But he added, “Speculation in this area will soon be a thing of the past.”
To support such optimism, researchers point to the recent discovery of so-called speciation genes. Most biologists define a species as a group that is reproductively isolated — it cannot interbreed or exchange genes with any other. The newly discovered genes cause reproductive isolation between two groups by causing their offspring, or hybrids, to be infertile or die....

2009 February 9. Darwinism Must Die So That Evolution May Live. By Carl Safina, The New York Times. Excerpt: Charles Darwin gets so much credit, we can’t distinguish evolution from him.
Equating evolution with Charles Darwin ignores 150 years of discoveries, including most of what scientists understand about evolution. Such as: Gregor Mendel’s patterns of heredity (which gave Darwin’s idea of natural selection a mechanism — genetics — by which it could work); the discovery of DNA (which gave genetics a mechanism and lets us see evolutionary lineages); developmental biology (which gives DNA a mechanism); studies documenting evolution in nature (which converted the hypothetical to observable fact); evolution’s role in medicine and disease (bringing immediate relevance to the topic); and more.
By propounding “Darwinism,” even scientists and science writers perpetuate an impression that evolution is about one man, one book, one “theory.”...

2009 February 9. Crunching the Data for the Tree of Life. By Carl Zimmer, The New York Times. Excerpt: Michael Sanderson..., a biologist at the University of Arizona, is part of an effort to figure out how all the estimated 500,000 species of plants are related to one another. For years now the researchers have sequenced DNA from thousands of species.... The pace of their progress gives Dr. Sanderson hope that they will draw the entire evolutionary tree of plants within the next few years....
There’s just one problem. “We have no way to visualize such a tree at the moment,” he said....
... Biologists have responded to the problem by enlisting the help of computer scientists and software designers from companies like Google and Adobe to find a new way of looking at evolution. Their goal is to create a program that allows scientists and nonscientists alike to fly through evolutionary trees....

2009 February 9. Seeing the Risks of Humanity’s Hand in Species Evolution. By CORNELIA DEAN, The New York Times. Excerpt: ...human predation is causing target species to evolve to reproduce at younger ages and smaller sizes, to their short-term benefit but to the long-term harm of the species.
...Because humans discovered fire, the benefits of hunting in teams and the bounties of agriculture, people have been changing the natural landscape, causing plants and animals to evolve in response....
...Human behavior has affected human evolution as well.... Since the beginning of the Industrial Revolution, humanity’s collective ability to change the world has been powered by fossil fuels and multiplied by machines. Often, the result has been evolutionary change at a fast pace and on a broad scale....

2009 February 9. Darwin the Comedian. Now That’s Entertainment! By JOHN TIERNEY, The New York Times. Excerpt: ...Officially, he is a science historian named Richard Milner, but he regularly turns into his hero on stage — complete with white beard, bowler and cape — in a one-man musical, “Charles Darwin: Live & In Concert.”...
“Everyone should find his own Darwin,” Mr. Milner says. “The man was so large. He was a zoologist, a botanist, an explorer, a travel writer, a philosopher, an abolitionist, a doting father, a radical intellectual revolutionary with an utterly conservative and blemish-free lifestyle. He revolutionized every field he touched, and he was trained in none of them.”
...Mr. Milner has turned the shy naturalist into a suavely bemused performer doing patter songs about trilobites, garfish and tortoise shells. (You can see excerpts at nytimes.com/science.)....

2007 June 29. Study Traces Cat’s Ancestry to Middle East. By Nicholas Wade. The New York Times. Excerpt: … [Carlos A. Driscoll of the National Cancer Institute and his colleagues have] spent more than six years collecting species of wildcat in places as far apart as Scotland, Israel, Namibia and Mongolia. He then analyzed the DNA of the wildcats and of many house cats and fancy cats. Five subspecies of wildcat are distributed across the Old World. … Their patterns of DNA fall into five clusters. The DNA of all house cats and fancy cats falls within the Near Eastern wildcat cluster, making clear that this subspecies is their ancestor… Wheat, rye and barley had been domesticated in the Near East by 10,000 years ago, so it seems likely that the granaries of early Neolithic villages harbored mice and rats, and that the settlers welcomed the cats’ help in controlling them. Unlike other domestic animals, which were tamed by people, cats probably domesticated themselves, which could account for the haughty independence of their descendants. … Until recently the cat was commonly believed to have been domesticated in ancient Egypt, where it was a cult animal. But three years ago a group of French archaeologists led by Jean-Denis Vigne discovered the remains of an 8-month-old cat buried with its human owner at a Neolithic site in Cyprus. …

2007 June 26. Fast-Reproducing Microbes Provide a Window on Natural Selection. The New York Times. By Carl Zimmer. Excerpt: In the corner of a laboratory at Michigan State University, one of the longest-running experiments in evolution is quietly unfolding. A dozen flasks of sugary broth swirl on a gently rocking table. Each is home to hundreds of millions of Escherichia coli, the common gut microbe. These 12 lines of bacteria have been reproducing since 1989, when the biologist Richard E. Lenski bred them from a single E. coli. “I originally thought it might go a couple thousand generations, but it’s kept going and stayed interesting,” Dr. Lenski said. He is up to 40,000 generations now, and counting. In that time, the bacteria have changed significantly. For one thing, they are bigger — twice as big on average as their common ancestor. They are also far better at reproducing in these flasks, dividing 70 percent faster than their ancestor. These changes have emerged through spontaneous mutations and natural selection, and Dr. Lenski and his colleagues have been able to watch them unfold.
When Dr. Lenski began his experiment 18 years ago, only a few scientists believed they could observe evolution so closely. Today evolutionary experiments on microbes are under way in many laboratories. And thanks to the falling price of genome-sequencing technology, scientists can now zero in on the precise genetic changes that unfold during evolution, a power previous generations of researchers only dreamed of. In the past century scientists have gathered a wealth of evidence about the power of natural selection. But much of that evidence has been indirect. In the late 1980s a few scientists began experimenting with microbes, hoping to observe natural selection in something closer to real time. Microbes can reproduce several times a day, and a billion of them can fit comfortably in a flask. Scientists can carefully control the conditions in which the microbes live, setting up different kinds of evolutionary pressures. Within a few hundred generations, Dr. Lenski was seeing changes, and the bacteria have been changing ever since. The microbes have adapted to their environment, reproducing faster and faster over the years. One striking lesson of the experiment is that evolution often follows the same path. “We’ve found a lot of parallel changes,” Dr. Lenski said. … Scientists have long known that underlying these visible changes were genetic ones. But only now are they documenting the mutations that allow this evolution to happen in the first place. …

2007 June 26. From a Few Genes, Life’s Myriad Shapes. The New York Times. By Carol Kaesuk Yoon. Excerpt: Since its humble beginnings as a single cell, life has evolved into a spectacular array of shapes and sizes... But just how such diversity of form could arise out of evolution’s mess of random genetic mutations … has remained one of the most fascinating and intractable questions in evolutionary biology. Now finally, after more than a century of puzzling, scientists are finding answers coming fast and furious and from a surprising quarter, the field known as evo-devo. Just coming into its own as a science, evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth. For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans.  “We’re still a very young field,” Dr. Gilbert said. “But I think this is a new evolutionary synthesis, an emerging evolutionary synthesis. I think we’re seeing it.”

2007 June 26. The Human Family Tree Has Become a Bush With Many Branches. By John Noble Wilford. The New York Times. Excerpt: Time was, fossils and a few stone artifacts were about the only means scientists had of tracing the lines of early human evolution. And gaps in such material evidence were frustratingly wide. When molecular biologists joined the investigation some 30 years ago, their techniques of genetic analysis yielded striking ...

2007 June 26. Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift. By Douglas H. Erwin. The New York Times. Excerpt: É Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science. The discovery of DNA marked one such shift, the theory of plate tectonics another. Éour evolutionary framework ... was constructed from the 1930s to 1950s by early geneticists, paleontologists and others, who disagreed about the efficacy of natural selection in driving evolutionary change (Darwin's big idea) and about the nature of the underlying genetic variation upon which natural selection could act. What they came to agree on was called the modern synthesis Éthat mutations to DNA create new variants of existing genes within a species. Natural selection, driven by competition for resources, allows the best-adapted individuals to produce the most surviving offspring. So adaptive variants of genes become more common. ÉIn the past few years every element of this paradigm has been attacked. Concerns about the sources of evolutionary innovation and discoveries about how DNA evolves have led some to propose that mutations, not selection, drive much of evolution, or at least the main episodes of innovation, like the origin of major animal groups, including vertebrates. The Achilles' heel of the modern synthesis, as noted by the philosopher Ron Amundson, is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history. ÉMost species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.
Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it....

Archive of Past Articles for Chapter 3

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