4. Inheritance

The Puzzle of Inheritance
2017-10-12. Genes for Skin Color Rebut Dated Notions of Race, Researchers Say. By Carl Zimmer, The New York Times.

2017-05-19. Genetic Tidying Up Made Humped Bladderworts Into Carnivorous Plants. By Joanna Klein, The New York Times.

2017-03-02. The Woolly Mammoth’s Last Stand. By Nicholas Wade, The New York Times.

2016-12-09. Rapid Evolution Saved This Fish From Pollution, Study Says. By Joanna Klein, The New York Times.

2016-11-15. European diseases left a genetic mark on Native Americans. By Michael Price, Science.

2016-10-29. Doubts About the Promised Bounty of Genetically Modified Crops. By Danny Hakim, The New York Times.

2016-05-17. Humans are still evolving—and we can watch it happen. By Elizabeth Pennisi, Science.

2015-12-04. Inside the summit on human gene editing: A reporter’s notebook. By John Travis, The New York Times.

2015-11-26. Open Season Is Seen in Gene Editing of Animals. By Amy Harmon, The New York Times.

2015-11-19. FDA approves AquaBounty Technologies' application to sell the genetically modified salmon to U.S. consumers. Wikipedia.

2015-06-19. The Sequencer is Mightier than the Sword. By Brian Palmer, onEarth, Natural Resources Defense Council.

2014-10-13. A Threat Is Seen in Pumas’ Isolation. By Douglas QuenQua, The New York Times.

2014-06-16. A Faster Way to Find the Origin of Malaria. Excerpt: By using a DNA “bar code” of 23 short snips from the genes of parasites that cause malaria, scientists can now often quickly determine where they originated, British researchers report. The information could be useful in fighting local outbreaks, which may be caused by parasites from other parts of the world. And it should be possible to make a test kit that will get that information from a spot of dried blood in two hours — far less time than is needed to sequence a whole genome. For the study, published on Friday in the journal Nature Communications, researchers from the London School of Hygiene and Tropical Medicine analyzed the DNA of more than 700 malaria-causing parasites from all over the world. For Plasmodium falciparum — the most dangerous species — they found 23 consistent mutations that let them tell, with 92 percent accuracy, whether a strain was from West Africa, East Africa, Southeast Asia, South America or the South Pacific. They still hope to find markers that distinguish strains from Central America, the Caribbean, southern Africa and the Indian subcontinent.... http://www.nytimes.com/2014/06/17/health/a-faster-way-to-find-the-origin-of-malaria.html. By Donald G. McNeil Jr, The New York Times.

2014-03-27. Custom Chromo: First Yeast Chromosome Built From Scratch. Excerpt: ...Using the labor of dozens of undergraduate students, scientists have built a customized yeast chromosome from scratch. It's a milestone in the rapidly growing field of synthetic biology, where organisms can be tailored for industrial use. In this case, the near-term goal is to understand the genetics of yeast, and eventually the genetics of us. This was quite an undertaking. Yeast have about 6,000 genes packed in 16 tidy bundles called chromosomes. Each chromosome is an enormous molecule of DNA packed in proteins. ...[Jef] Boeke and his colleagues put together a class, called Build-A-Genome, and got undergraduates at Hopkins to do the painstaking labor of constructing long strings of DNA. These would eventually become segments of their yeast chromosome. ...To make the chromosome useful for research, they've deleted some parts of the DNA that they believe are not essential, "and then we add a number of bells and whistles to the chromosome, that we think will make for a more interesting version that we can play evolutionary games with in the laboratory," Boeke says. ...Of course, this deep manipulation of DNA also raises ethical questions — about everything from patenting life-forms, to the potential misuse of biotechnology for weapons or other nefarious purposes. So part of the class involved an ethics discussion, led by Debra Mathews, a bioethicist at Johns Hopkins.... http://www.npr.org/blogs/health/2014/03/27/295260600/custom-chromo-first-yeast-chromosome-built-from-scratch. Richard Harris, NPR.

2013-12-04. Baffling 400,000-Year-Old Clue to Human Origins.    Excerpt: ...In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years. The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found. ...“The more we learn from the DNA extracted from these fossils, the more complicated the story becomes,” Dr. Shapiro said. This complicated story has come to light only because of advances over the past 20 years in retrieving ancient DNA. When an organism dies, its DNA breaks down into smaller and smaller fragments, while also becoming contaminated with the DNA of other species like soil bacteria. So piecing the fossil DNA together is a bit like putting together a jigsaw puzzle created by a sadist.... http://www.nytimes.com/2013/12/05/science/at-400000-years-oldest-human-dna-yet-found-raises-new-mysteries.html, Carl Simmer, The New York Times.

2013-07-27.  A Race to Save the Orange by Altering Its DNA. Excerpt: ...The disease that sours oranges and leaves them half green, already ravaging citrus crops across the world, had reached .. [Florida's] groves. ...Florida growers who supply most of the nation’s orange juice poured everything they had into fighting the disease they call citrus greening. ... “In all of cultivated citrus, there is no evidence of immunity,” the plant pathologist heading a National Research Council task force on the disease said. In all of citrus, but perhaps not in all of nature. ...They would have to alter the orange’s DNA — with a gene from a different species.  ...the idea of eating plants and animals whose DNA has been manipulated in a laboratory — called genetically modified organisms, or G.M.O.’s — still spooks many people. Critics worry that such crops carry risks not yet detected, and distrust the big agrochemical companies that have produced the few in wide use. .... http://www.nytimes.com/2013/07/28/science/a-race-to-save-the-orange-by-altering-its-dna.html. Richard Perry, The New York Times.

2012-12-21. Engineered Fish Moves a Step Closer to Approval | Andrew Pollack, The New York Times. Excerpt: Government regulators moved a big step closer on Friday to allowing the first genetically engineered animal — a fast-growing salmon — to enter the nation’s food supply. The Food and Drug Administration said it had concluded that the salmon would have “no significant impact” on the environment. The agency also said the salmon was “as safe as food from conventional Atlantic salmon.” … The AquAdvantage salmon… is an Atlantic salmon that contains a growth hormone gene from the Chinook salmon and a genetic switch from the ocean pout, an eel-like creature. The switch keeps the gene on so that the salmon produces growth hormone year round, rather than only during warm weather. The fish reach market weight in about 18 months instead of three years. … The main concern addressed was whether the genetically engineered salmon could escape and establish themselves in the wild, with detrimental environmental consequences. The larger salmon, for instance, could conceivably outcompete wild Atlantic salmon for food or mates.  The agency said the chance this would happen was “extremely remote.” It said the salmon would be raised in inland tanks with multiple barriers to escape. Even if some fish did escape, the nearby bodies of water would be too hot or salty for their survival. And reproduction would be unlikely because the fish would be sterilized, though the sterilization technique is not foolproof…. Read the full article: http://www.nytimes.com/2012/12/22/business/gene-altered-fish-moves-closer-to-federal-approval.html?nl=todaysheadlines&emc=edit_th_20121222&_r=0

2012 Sept 05. Bits of Mystery DNA, Far From 'Junk,' Play Crucial Role to Health. By Gina Kolata, The NY Times. Excerpt: Among the many mysteries of human biology is why complex diseases like diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease like cancer or depression, while an identical twin remains perfectly healthy. Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches…. 

2012 Aug 27. As Genes Learn Tricks, Animal Lifestyles Evolve. By Sean B. Carroll, The NY Times. Excerpt: Changes in the structure of the TRPA1 receptor, and the evolution of very high levels of expression in their sensory pits, endowed [snakes] with sensitive infrared detectors. The large evolutionary distance between pit vipers and pythons and boas indicates that the two groups of snakes separately evolved infrared sensing. But TRPA1 is not the only means of infrared sensing…blood-feeding bats also has sensory pits around the noses that the animals use to locate the warmest areas on the surface of their furry prey, where blood flow is the greatest…recruit[ing] a different ion channel/ receptor called TRPV1 to become an infrared sensor. What is especially noteworthy about TRPV1 is that it is the very same receptor that detects capsaicins, the active ingredients in chili peppers, in our neurons. It causes the familiar burning sensation when prompted… scientists discovered that the particular form of the receptor expressed in vampire bat trigeminal neurons was much more heat-sensitive (by about 9 degrees Celsius) than either our TRPV1 receptor or the TRPV1 expressed in fruit bat neurons. The vampire bat receptor is thus tuned to detect heat in ways that other bats and mammals cannot. Both the TRPA1 and TRPV1 genes are hundreds of millions of years old, having arisen deep in evolutionary history, while vampire bats, pit vipers, and pythons and boas are much younger species. The histories of these genes and animals, and the repeated invention of infrared sensing, demonstrate how the evolution of new abilities does not necessarily require new genes, but new variations of very old genes and new ways of using them….

2012 May 3. Island’s Genetic Quirk: Dark Skin, Blond Hair by SINDYA N. BHANOO, The NY Times. Excerpt: In the Solomon Islands, about 10 percent of the dark-skinned indigenous people have strikingly blond hair. Some islanders theorize that the coloring could be a result of excess sun exposure, or a diet rich in fish. Another explanation is that the blondness was inherited from distant ancestors — European traders and explorers who came to the islands. About 10 percent of indigenous people in the Solomon Islands have a gene variant for blond hair. But that’s not the case… The gene variant responsible for blond hair in the islanders is distinctly different from the gene that causes blond hair in Europeans….

2012 May 7. It's Not So Lonely at the Top: Ecosystems Thrive High in the Sky by CARL ZIMMER, The NY Times. Excerpt: Looming over the northern edge of the Amazon rain forest are some of the most remarkable mountains on earth. Known as tepuis, or tabletop mountains, they are typically ringed by sheer cliffs that rise thousands of feet from the surrounding lowland jungles….They are like islands in the sky, covered with low forests and shrublands that support a diversity of animals likes frogs and lizards….Even more intriguing than the tepuis’ long isolation is that many species living atop them are found nowhere else. To many biologists, the only explanation that made sense was that the ancestors of those unique animals and plant species have lived on the tepuis for more than 70 million years. In honor of Conan Doyle, they called this notion the “lost world hypothesis.”….

2011 October 17.  From Telomeres to the Origins of Life. By Claudia Dreifus, The NY Times.  [An interview with biochemist and 2009 Nobel Laureate Dr. Jack W. Szostak] Excerpt:
Q: [What did you and Elizabeth H. Blackburn discover about telomeres together?]
A: ...We figured out the underlying biochemistry and showed that lots of different organisms use that biochemistry. We figured out that there was an enzyme, telomerase, that adds DNA to the ends of chromosomes to balance out the DNA that is naturally lost as cells grow.
Afterward, as people in the field began to see how important it was, telomere research just took off. It became clear that the loss of DNA from telomeres might have something to do with aging. Subsequently, it’s turned out that in almost all cancers, telomerase is turned on so those cells grow indefinitely. Of course, it’s very nice that work we did so long ago turned out to be important! ….
Q: …What do you study now?
A: The origins of life. In my lab, we’re interested in the transition from chemistry to early biology on the early earth... The way that we study that is by trying to make it happen in the lab. We take simple chemicals and put them together in the right way. And we’re trying to build a very, very simple cell that might look like something that might have developed spontaneously on the early earth….

2010 September. Sex and the Single Chromosome. By Kathleen M. Wong, Science Matters @ Berkeley. Excerpt: ...Doris Bachtrog, a Berkeley professor of integrative biology, studies how sex chromosomes evolve these differences. Her approach is to compare related species whose sex chromosomes emerged at different times. ....Bachtrog’s comparisons of various fruit fly species demonstrate that Y chromosomes accumulate specific defects over time.

2010 July 19. Birds Choose Different Path to Manage Their Sexes. By Nicolas Wade, The New York Times. Excerpt: ...In a series of experiments over the past 15 years, David Page of the Whitehead Institute has reconstructed many of the steps in the evolution of the human sex chromosomes, which he calls “an infinitely rich experiment of nature.” He has now started to analyze a parallel experiment, the sex chromosomes of birds.
…In humans, men have an X and a Y chromosome, and women two X’s. In reptilian times, the X and the Y were an ordinary pair of chromosomes until the male-determining gene landed on the Y. Thereupon the Y started shedding the genes it held in common with the X and shriveled to a fraction of its former size.
Birds have evolved a similar system with a twist — it’s the male that has two of the same chromosomes. Their sex chromosomes are called the Z and W, with males having two Z’s and females a Z and a W. The Z and W are derived from a different pair of ancestral chromosomes than the X and Y, a team led by Daniel W. Bellott and Dr. Page report in the current issue of Nature. The Z’s evolution has in several ways paralleled that of the X, even though each is associated with a different sex.
…Masculinity in people is attained with a single Y, so why do male birds need two Z’s? The solution was found last year by a group led by Craig A. Smith and Andrew H. Sinclair of the Royal Children’s Hospital in Melbourne, Australia. In humans, the default condition is female and the reproductive organs develop as male in the presence of the male-determining gene’s protein.
In birds, sex is determined by the dose of the sex gene, which the Melbourne team identified as one called DMRT1. Bird embryos exposed to a single dose develop as female; two copies of the gene make a male.
...“I see an endless chain of revelations in the future that will come from comparing the human X and Y to other sex chromosomes of species at different evolutionary distances,” Dr. Page said.

2010 May 31. A Family Feud Over Mendel's Manuscript on the Laws of Heredity. By Nicholas Wade, NY Times. Excerpt: …The manuscript is the account by Gregor Mendel of the pea-breeding experiments from which he deduced the laws of heredity and laid the foundations of modern genetics.
…The priceless manuscript was discarded in 1911 by the Brünn Natural History Society and, luckily, rescued by a local high school teacher who retrieved it from a wastepaper basket in the society’s library…
…At some point after 1988, Erich Richter, a Mendel descendant who is also an Augustinian monk known as Father Clemens, told other family members that he possessed Mendel’s manuscript. It had been sent to him by a monk in Prague and he wanted to place it legally in the family’s possession. So in 2001, eight senior members of the Mendel family — including Father Clemens — formed a company to preserve the document as a German cultural treasure, and the manuscript was placed in a safe deposit box in a bank in Darmstadt, Germany.
...Father Clemens began to change his story about the ownership of the manuscript, suggesting it really belonged to the Augustinians, said William Taeusch, Dr. Schmidt’s husband. “He started to say to the family, ‘Aren’t they the rightful owners?’ The family says, ‘What’s going on, for God’s sake? If you were given it and were told it was the Augustinians’ property, why did you keep it for yourself for 11 years and then sign a bogus contract giving it to the family?’ ”

2010 Mar 11. Disease Cause Is Pinpointed With Genome. By Nicholas Wade, New York Times. Excerpt: Two research teams have independently decoded the entire genome of patients to find the exact genetic cause of their diseases....
In the decade since the first full genetic code of a human was sequenced for some $500 million, less than a dozen genomes had been decoded, all of healthy people.
Geneticists said the new research showed it was now possible to sequence the entire genome of a patient at reasonable cost and with sufficient accuracy to be of practical use to medical researchers....
In one case, Richard A. Gibbs of the Baylor College of Medicine sequenced the whole genome of his colleague Dr. James R. Lupski, a prominent medical geneticist who has a nerve disease, Charcot-Marie-Tooth neuropathy....

2010 Feb 17. Scientists Decode Genomes of Five Africans, Including Archbishop Tutu. By Nicholas Wade, NY Times. Excerpt: The complete genomes of five southern Africans have been decoded, almost doubling the number of published human DNA sequences. The Africans include four Bushmen hunter-gatherers, known as !Gubi, G/aq’o, D#kgao and !Ai, the odd symbols representing different clicking sounds in Bushmen languages. The fifth person, a Bantu, is none other than Archbishop Desmond Tutu.
...African genomes are of particular interest for understanding human genetic history because they have more variation in their DNA than other populations. Everyone outside Africa is descended from a small group that left some 50,000 years ago, carrying away only a small sample of the available genetic diversity....
...Geneticists are interested in variations in the human DNA sequence because these underlie human diversity, including susceptibility to disease. The Pennsylvania team found 1.3 million novel DNA variants in its five Africans, and some 13,000 new changes in those parts of the DNA that specify proteins, the working parts of living human cells....

2009 March 3. A Call for Resilient Farms in Warming World. By Andrew C. Revkin, The NY Times. Excerpt: In the icy gloom of Norway’s Arctic archipelago, scientists gathered last week to celebrate the first anniversary of the Svalbard Global Seed Vault, an archive of the world’s agricultural genetic diversity carved into the frigid earth. I got a “post card” over the weekend from one participant, Nina Fedoroff, the science and technology adviser to the secretary of state and to administrator of the United States Agency for International Development.
Dr. Fedoroff is a longstanding proponent of probing and exploiting genes to make crops and livestock more productive and less vulnerable to pests and climate extremes. This puts her at odds with some environmentalists and European governments.
Her full dispatch...is focused on the importance of preserving and exploiting genetic diversity as a way to sustain food production in the face of both growing human populations and appetites (prosperity still tends to boost peoples’ appetite for meat) and rising dangers from warming driven by accumulating greenhouse gases....


2009 February 29. A worldwide pollutant may cause gene loss. By Niladri Basu, Environmental Health News. Excerpt: A new study suggests that long term exposure to a common water pollutant reduced the genetic diversity of the midge - a common water insect.
Aquatic insects are the foundation of healthy waterways. Other insects, invertebrates and fish depend on the tiny creatures for food. A loss of their genetics is a loss for ecosystem diversity.
The pollutant, called tributyltin (TBT), is a widely used pesticide. While TBT affected the growth, survival and reproduction of the midge insect, the greatest effects were found in the genes. TBT-exposed insects lost gene diversity two times greater than non-exposed insects.
The study provides direct evidence from the lab that pollution may cause genetic loss in nature....
Genetic diversity is the number of different kinds of genetic characteristics in a species. Genes govern an individual's characteristics -- whether external appearances or internal functions. Diversity ensures that a population has a large number of gene variations spread among individuals.
...Before its recent worldwide ban, TBT was used extensively in marine paints to keep barnacles and other marine creatures from growing on ship hulls. In the environment, TBT does not break down and it builds up in food chains. Because of its longevity and widespread use, it is no surprise that TBT pollutes harbors, waterways and animals all over the world....

2008 July/August. Tracing Evolution in Genes. By Kathleen M. Wong, ScienceMatters@Berkeley. Excerpt: How do humans differ from chimpanzees? ...we're taller, less hairy, and-a point no one fails to mention-far brainier than our closest primate relatives.
All of these differences and more have emerged over the past five million years, when the common ancestor of both species reached an evolutionary fork in the road. How early hominids came to walk the savannah, while early chimpanzees returned to the forests, has fascinated professional scientists and armchair anthropologists alike.
The best way to answer those questions, according to Rasmus Nielsen, is to study our respective genomes. "Evolutionary biology is an historical science," says Nielsen, a Berkeley professor of integrative biology. "But in the absence of a time machine, we can't really go back and show exactly why certain evolutionary events occurred. All we have to work with is what we observe today. So we look at the DNA to see the evidence for past Darwinian selection."
Nielsen uses the power of statistics and computing to compare the DNA of different species or populations. By identifying which sets of genes have changed, or mutated, he can describe how ancestral populations diverged step by tiny genetic step. His work not only recasts the story of human evolution but promises to uncover the genetic roots of many diseases...


2008 May. Distant Relatives, Common Genes. By Kathleen M. Wong, ScienceMatters@Berkeley. Excerpt: Glance through any family's photo album, and you're likely to home in on a few outstanding ancestral traits. The shape of a nose or the arch of an eyebrow can be passed down for generation after generation.
Biologists have long studied commonalities such as these to infer ancestral relationships between animals. But the more distant the relationship, such as between humans and sponges, the trickier it is to establish connections through simple comparisons of anatomy.
Dan Rokhsar, a Berkeley professor of both physics and molecular and cellular biology, and a faculty scientist at the Department of Energy's Joint Genome Institute, is sidestepping this problem via a different aspect of inheritance: genes. Genes shared by distantly related animals are likely to have originated in their last common ancestor. So by sequencing and comparing the genomes of creatures ranging from sea anemones to sea squirts, limpets to pufferfish, Rokhsar and his research team hope to reconstruct characteristics of the great-great grandparents to all animals.
"We're interested in that transition from being a unicellular organism to being multicellular-when it happened and how it happened," Rokhsar says…
Recently, the skyrocketing price of petroleum and the threat of global climate change have turned Rokhsar's attention toward greener subjects: plants…
"The cellulose and lignin in plant walls is where all of the carbon goes from photosynthesis. That's the carbon we want to convert to fuel. How do they do it? One way to find an answer is to look at genomes," Rokhsar says.
He is now working to sequence the genome of switchgrass, a native plant and strong candidate to produce biofuel…
"We need to collapse the 5,000 years it took to breed maize into an edible plant into 10 years for switchgrass, because we don't have a lot of time to develop renewable fuels," Rokhsar says. "And we'll need to do this sustainably and as a solution for the long term."

2008 April 22. Expressing Our Individuality, the Way E. Coli Do. By CARL ZIMMER, The NY Times. Excerpt: We humans differ from one another in too many ways to count...Scientists have only a rough understanding of how this diversity arises… We put a far bigger premium on nature than nurture when it comes to our individuality. That’s one reason why reproductive cloning inspires so much horror. If genes equal identity, then a person carrying someone else’s DNA has no distinct self. But there’s a deep flaw in this way of thinking, one that blinds us to how biology — human or otherwise — really works. A good counterexample is E. coli, a species of bacteria that lives harmlessly in every person’s gut by the billions. A typical E. coli contains about 4,000 genes (we have about 20,000). Feeding on sugar, the microbe grows till it is ready to split in two. It makes two copies of its genome, almost always managing to produce perfect copies of the original. The single microbe splits in two, and each new E. coli receives one of the identical genomes. These two bacteria are, in other words, clones...E. coli expresses its individuality in many other ways, as well…These quirks of E. coli’s personality can mean the difference between life and death for the bacteria. In times of stress, some members of a colony respond by building thousands of toxin molecules and then burst open, killing off the unrelated E. coli around them. Their fellow clones survive, though, and thrive without the competition.
The key to understanding E. coli’s fingerprints is to recognize that the bacteria are not simple machines. Unlike wires and transistors, E. coli’s molecules are floppy, twitchy and unpredictable. In an electronic device, like a computer or a radio, electrons stream in a steady flow through the machine’s circuits, but the molecules in E. coli jostle and wander. When E. coli begins using a gene to make a protein, it does not produce a smoothly increasing supply. It spurts out the proteins in fits and starts. One clone may produce half a dozen copies of a protein in an hour, while a clone right next to it produces none.
Other studies suggest that the unpredictable noisiness in E. coli’s cellular machinery is also responsible for persistence, hairy coats, selfless suicide and vulnerability to viruses. The big question for many scientists is why E. coli has evolved so that noise can produce such drastic changes in its biology…
Identical genes can also behave differently in our cells because some of our DNA is capped by carbon and hydrogen atoms called methyl groups. Methyl groups can control whether genes make proteins or remain silent. In humans (as well as in other organisms like E. coli), methyl groups sometimes fall off of DNA or become attached to new spots. Pure chance may be responsible for changing some methyl groups; nutrients and toxins may change others.
…At the very least, E. coli’s individuality should be a warning to those who would put human nature down to any sort of simple genetic determinism. Living things are more than just programs run by genetic software. Even in minuscule microbes, the same genes and the same genetic network can lead to different fates.

2008 March 4. Gene Map Becomes a Luxury Item. by Amy Harmon. The New York Times. Excerpt: Dan Stoicescu, 56, a biotechnology entrepreneur who retired two years ago after selling his company, became the second person in the world to buy the full sequence of his own genetic code paying $350,000 price tag. Scientists have so far unraveled only a handful of complete human genomes, all financed by governments, foundations and corporations in the name of medical research.
But while money may buy a full readout of the six billion chemical units in an individual’s genome, biologists say the superrich will have to wait like everyone else to learn how the small variations in their sequence influence appearance, behavior, abilities, disease susceptibility and other traits.
Biologists have mixed feelings about the emergence of the genome as a luxury item. Some worry that what they have dubbed “genomic elitism” could sour the public on genetic research that has long promised better, individualized health care for all. But others see the boutique genome as something like a $20 million tourist voyage to space — a necessary rite of passage for technology that may soon be within the grasp of the rest of us.
Scientists say they need tens of thousands of genome sequences to be made publicly available to begin to make sense of human variation.
Mr. Stoicescu, who wants to create an open database of genomic information seeded with his own sequence, hopes others will soon join him.

2008 February. Statistical Challenges in Genomics. by Kathleen M. Wong, ScienceMatters@Berkeley ...Called a DNA microarray, it is a miniature laboratory on a chip. In a single experiment it can deliver a detailed snapshot of the thousands of genes and proteins interacting in an organism, whether bacterium or human.For biologists, DNA microarrays have been boon and curse alike. Researchers routinely use these assays to monitor gene expression patterns in cells from cancer patients, with the aim of deriving better diagnosis and treatment strategies for the disease. They can now obtain unprecedented insights into the activities of genes and cells with a minimum of experimental effort. At the same time, they are struggling to make sense of the tidal wave of data that ensues. "Each microarray experiment yields thousands and thousands of measurements for just one person," says Sandrine Dudoit, a Berkeley professor of Biostatistics and Statistics. "Microarrays and other high-throughput biological assays are raising challenging statistical design and analysis questions and are a driving force for our discipline. The scale and complexity of the data are unprecedented and far greater than traditional methods allow you to handle." ...Dudoit specializes in developing statistical and computational methods to analyze and comprehend the mind-bogglingly large and intricate datasets generated by high-throughput biotechnologies such as DNA microarrays. ...She develops statistical methods to uncover relationships among a patient's entire genome; demographic and environmental variables such as age, sex, ethnicity, and diet; and medical outcomes such as survival prognosis and response to treatment. ...With a next generation of DNA sequencing machines entering the scene, we are facing new and even greater statistical and computational challenges," Dudoit says. "You feel like your work really matters; it's being applied immediately, with the goal of elucidating fundamental scientific questions and improving public health."

2008 February. Gene escapes to weeds from engineered canola. Union of Concerned Scientists newlstter. A recent study found that canola plants in Quebec, Canada, that were genetically engineered for herbicide resistance have interbred with a weed called wild mustard, producing hybrid plants that are resistant to the herbicide glyphosate. The herbicide-resistance gene persisted over five generations and spread from the hybrids into the mustard weeds, in spite of the fact that no herbicide was applied to the area. The event is significant for two reasons. One, it is the first known escape of a gene from a commercialized genetically engineered crop into a weed. Two, because canola is a major crop, covering an estimated two million acres across Canada, it is likely that gene escape has occurred at multiple sites in addition to the few that were monitored. The event echoes the escape of a gene for glyphosate resistance from field trials of bentgrass into wild relatives (see our previous story). Inadequate confinement of engineered crops may harm ecosystems in some circumstances and may hasten the development of herbicide-resistant weeds. Read the abstract describing the study in the scientific journal Molecular Ecology.

January 2008. The Copy Machine of the Cell
by Kathleen M. Wong. Excerpt: There comes a
time in many a cell's life when it feels the need to reproduce. But
before it can split into two, it must fashion a second set of genetic instructions to pass on to the new cell. When Berkeley professor of biochemistry and molecular biology Mike Botchan first began studying chromosome copying, basic questions about the process remained unknown. He wanted to understand how and where DNA replication began. Over the past three decades, Botchan has been instrumental in piecing together the story of what he calls "the elaborate dance of replication." Botchan began by studying viruses, the simplest of all life forms. These microbes contain relatively few genes in their chromosome, borrowing much of the machinery needed to duplicate their own DNA from host cells. ...To decipher the string of events required to start replication, Botchan mapped the initiation site-a place on a chromosome where replication begins-in a virus. He found that a certain DNA sequence attracts a virus protein involved in replication initiation. Only then can the virus helicase, which unwinds and separates the strands of DNA, bind to the chromosome and start unraveling DNA....
But do more complex organisms, such as insects and humans, copy their DNA in a similar fashion? To find out, Botchan studied a case of unchecked DNA replication in fruit fly embryos. The cells that go on to form the fly's eggshell duplicate certain sections of their DNA with astonishing rapidity, initiating replication at many sites at
once. In these cells, Botchan found and characterized a complex of proteins that finds the initiation site and prepares the chromosome so that a core replication machine can be assembled there. The core replication machine includes a six-protein complex used at all DNA replication sites. Several of these proteins form a pinwheel structure that encircles DNA, while another links to the polymerase enzyme that "reads" the sequence. In cells actively copying their
DNA, all of these proteins are located right on top of one another.
...Botchan's work, along with research by Berkeley biologists Eva
Nogales and James Berger, helps prove that DNA replication has
changed very little across evolution. "All three kingdoms of life
share a basic core machinery that assembles on DNA and prepares it for unwinding," Botchan says. Organisms ranging from E. coli to fruit flies, they find, have nearly identical chromosome copying methods, cementing the relationship of all life forms back to that first ancestral cell.

October 2007 The Mathematician and the Genome. By Kathleen M. Wong, ScienceMatters@Berkeley.
Excerpt: ...The completion of the Human Genome Project in 2001 was hailed as a major breakthrough in science. For the first time, humans could look at their DNA and discover traits ranging from their propensity to alcohol addiction to the likelihood that their children will have blue eyes.
...Since then, scientists have added the rat, cow, chicken, dog, and even platypus to the list of creatures whose genes have been read like a biochemical book. Each species has shed new light on the structure and function of our own genetic code.
Lior Pachter has been at the forefront of these new genomic analyses. Officially a UC Berkeley professor of mathematics and computer science, Pachter considers himself a mathematical biologist. He uses the power of mathematical modeling and statistics to evaluate the vast quantities of data in DNA.
...Pachter likens genome studies to recreating plans for an existing building. "Until now, we've just been labeling the parts, the doorknobs and windows. Only recently have we started to ask about the function of the parts, and how these functions are related to each other."
...In addition to sequence data, a profusion of other genetic information is now flooding the field. Measurements of gene expression in different tissues, ways to measure gene variations between individuals, and other information can all help make sense of how our DNA makes us who we are. "Mathematics and statistics provides a good means for synthesizing the data in a reasonable way," Pachter says.
Just this year, Pachter began collaborating on the Human Microbiome Project. This new initiative from the National Institutes of Health seeks to analyze the microbial flora that lives in and on the human body. Scientists estimate that each person carries around 10 times more bacterial than human cells, species ranging from helpful gut microbes to pathogens like streptococci. The project will generate a jumble of gene fragments from both known and new species. Pachter's role is to help determine the rough number of creatures represented in the mix.
"It's fun for me that I can combine both mathematics and biology and participate in these major enterprises," Pachter says. "The best thing is, I get to do a lot of beautiful math to go along with it."

26 June 2007. Human DNA, the Ultimate Spot for Secret Messages (Are Some There Now?). The New York Times. ByDennis Overbye. Excerpt: … Using the same code that computer keyboards use, the Japanese group, led by Masaru Tomita of Keio University, wrote four copies of Albert Einstein’s famous formula, E=mc2, along with “1905,” the date that the young Einstein derived it, into the bacterium’s genome, the 4.2-million-long string of A’s, G’s, T’s and C’s that determine everything the little bug is and everything it’s ever going to be. The feat, they said in a paper published in the journal Biotechnology Progress, was a demonstration of DNA as the ultimate information storage material, able to withstand floods, terrorism, time and the changing fashions in technology, not to mention the ability to be imprinted with little unobtrusive trademark labels — little “Made by Monsanto” tags, say. In so doing they have accomplished at least a part of the dream that Jaron Lanier, a computer scientist and musician, and David Sulzer, a biologist at Columbia, enunciated in 1999. To create the ultimate time capsule as part of the millennium festivities at this newspaper, they proposed to encode a year’s worth of the New York Times magazine into the junk DNA of a cockroach. “The archival cockroach will be a robust repository,” Mr. Lanier wrote, “able to survive almost all conceivable scenarios.” …

June 2007. Looking Deep, Deep Into Your Genes. OnEarth, NRDC. by Laura Wright. Excerpt: Discoveries about the impact of the environment on our DNA could revolutionize our concept of illness. ...Although some diseases are inherited through a single genetic mutation -- cystic fibrosis and sickle cell anemia are examples -- the classic "one gene, one disease" model doesn't adequately explain the complex interplay between an individual's unique genetic code and his or her personal history of environmental exposures. That fragile web of interactions, when pulled out of alignment, is probably what causes many chronic diseases: cancer, obesity, asthma, heart disease, autism, and Alzheimer's, to name just a few....
...The completion of the Human Genome Project in 2003 armed scientists with a basic road map of every gene in the human body, allowing them to probe more deeply into the ways our DNA controls who we are and why we get sick, in part by broadening our understanding of how genes respond to external factors.
...In 2001, Jennifer Sass, a neurotoxicologist and senior scientist at the Natural Resources Defense Council (NRDC), who was then a postdoctoral researcher at the University of Maryland, designed an experiment that included the use of microarrays and other molecular tools to figure out how, exactly, mercury was interfering with both our nervous and immune systems. ...The findings of Sass, Silbergeld, and others indicate that mercury might play a role in the development of diseases involving immune system dysfunction. These diseases perhaps include autism ... but also the spate of autoimmune disorders that we can't fully explain, from Graves' disease and rheumatoid arthritis to multiple sclerosis and lupus.
"Do we need to reevaluate our fish advisories?" Silbergeld asks. "Are our regulations actually protecting the most sensitive people?" We target pregnant women and children because we've presumed that mercury's neurotoxic effects are most damaging to those whose brains are still developing. Sass and Silbergeld's findings don't contradict that assumption, but they do suggest that there might be other adults who are far more vulnerable than we'd realized -- who simply can't tolerate the more subtle effect the metal has on their immune system because of a peculiarity in their genetic makeup. Designing fish advisories for those people, whose sensitivities are coded in their DNA, is a challenge we've never tackled before....

23 May 2007. Study: Climate Change Could Harm CropsBy THE ASSOCIATED PRESS. Excerpt: ROME (AP) -- ...During the next 50 years, more than 60 percent of 51 wild peanut species analyzed and 12 percent of 108 wild potato species analyzed could become extinct because of climate change, according to a study released Tuesday by the Consultative Group on International Agricultural Research. Surviving species would be confined to much smaller areas, further eroding their capacity to survive, the report said. The study looked at the distribution of various species and predicted their ability to survive based on current and projected climate data for 2055. Farmers and researchers often depend on wild plants to breed new varieties of crops that contain genes for traits such as pest resistance or drought tolerance, and that reliance is expected to increase as climate changes strain the ability of crops to continue to have the same yields as now, the group said in a statement. In recent years, genes found in wild relatives have helped develop new types of domesticated potatoes that can fight devastating potato blight and new varieties of wheat more likely to survive droughts, the statement said. ''There is an urgent need to collect and store the seeds of wild relatives in crop diversity collections before they disappear,'' said Andy Jarvis, an agricultural geographer who led the study. ''At the moment, existing collections are conserving only a fraction of the diversity of wild species that are out there.'' ....Consultative Group on International Agricultural Research: http://www.cgiar.org

5 September 2006. This Can't Be Love. By CARL ZIMMER. NY Times. Across the eastern United States, a gruesome ritual is in full swing. The praying mantis and its relative, the Chinese mantis, are in their courtship season. A male mantis approaches a female, flapping his wings and swaying his abdomen. Leaping on her back, he begins to mate. And quite often, she tears off his head. The female mantis devours the head of the still-mating male and then moves on to the rest of his body. ...Sexual cannibalism has fascinated biologists ever since Darwin. It is not limited to mantises, but is also found in other invertebrates, including spiders, midges and perhaps horned nudibranchs. Biologists have debated how this behavior has evolved in these species. Some have suggested that sexual cannibalism is just a result of a voracious female appetite. But experiments have also suggested that it is a strategy that females use to select the best fathers for their offspring....

11 October 2005. In the Classification Kingdom, Only the Fittest Survive. By CAROL KAESUK YOON. NY Times. Carolus Linnaeus, the 18th-century botanist and father of scientific naming, enjoyed the unusual status of international scientific hero. Celebrated as the creator of a classification system that ... uses kingdoms of life and two-part Latin names for species, was so complete that it seemed he had forever solved the problem of cataloging the world's living things. So Linnaeus would most likely be shocked - after guessing there were fewer than 15,000 species of animals and plants on earth - to learn that more than 200 years later, scientists are far from finishing the naming of living things and are once again being overwhelmed by an explosion of new species and names. Between 1.5 million and 2 million species have been named, and a deluge of what could be millions more appears imminent. As a result, scientists have once again been seized by 18th-century paroxysms of fear that the field of classification could descend into chaos with precious information lost. For while the Linnaean method for organizing life is still followed and has held up well, no one oversees what has become the rapid and sometimes haphazard proliferation of species names.

19 March 2005. Latest research into the X chromosome brings startling discoveries. The Scotsman. by ROBERT LEE HOTZ. SCIENTISTS have found genetic evidence for what some men have long suspected: it is dangerous to make assumptions about women. The key is the X chromosome, the "female" sex chromosome that all men and women have in common. In a study published this week in the journal Nature, scientists said they had found an unexpectedly large genetic variation in the way parts of women's two X chromosomes are distributed among them. The findings were published in conjunction with the first comprehensive decoding of the chromosome. Females can differ from each other almost as much as they do from males in the way many genes at the heart of sexual identity behave, researchers say. "Literally every one of the females we looked at had a different genetic story," says Duke University genetics expert Huntington Willard, who co-wrote the study. "It is not just a little bit of variation." ...The newly discovered genetic variation between women might help account for differing gender reactions to prescription drugs and the heightened vulnerability of women to some diseases, experts say. ...All told, men and women may differ by as much as 2 per cent of their entire genetic inheritance, greater than the hereditary gap between humankind and its closest relative, the chimpanzee. "In essence," Willard says, "there is not one human genome, but two: male and female." ...The X chromosome contains a larger share of genes linked to disease than any other chromosome. It is implicated in 300 hereditary disorders, including colour blindness, haemophilia and Duchenne muscular dystrophy. Nearly 10 per cent of the genes may belong to a group known to be more active in testicular cancers, melanomas and other cancers, the team reports.

3 May 2005. NASA RELEASE: 05-115. NASA and EPA Team to Improve Crop Management. Can you see the difference between traditional corn and bio-engineered corn? NASA technology is beginning to provide the answer in a snapshot. The technology is called hyperspectral imaging. It uses a special camera to cut one snapshot into 120 color-specific images. Hyperspectral means getting many more images within the spectrum of just one picture. Each image shows a unique characteristic not visible to the human eye. ...The Environmental Protection Agency (EPA) teamed with NASA to use the technology to ensure appropriate management practices are used to avoid the development of resistance in corn pest populations. Pest resistance could severely limit the continued use of these new varieties of corn. With more than 25 million acres of corn planted this year, it is physically and economically infeasible to sample each one. This new technology seeks to provide an active monitoring capability to inform the grower of pest resistance development. Early use of hyperspectral imaging provides the ability to distinguish between the two types of corn and identify pest infestation conditions. Bio-engineered corn has inserted genes to make the plant resistant to insects. ..."This effort will enhance NASA's understanding of image processing techniques to extract knowledge from hyperspectral data sets," said Brian Mitchell of NASA's Space Partnership Development Program at Marshall. "The research being conducted with genetically modified plants and plant growth has the potential to contribute significantly in our ability to grow sustainable and nutritional crops in space. This could prove vital for long duration exploration missions." ...Hyperspectral imaging may be used to treat crew injuries in space. The Institute is working on a portable, handheld camera to take images of a wound site. Using that image to identify wound severity and healing progress will allow doctors to decide the best treatment. The imaging could save precious diagnostic time, which would also improve healing by ensuring timely and proper treatment. Hyperspectral imaging will also detect mold and toxins in spacecraft, a needed tool during long-duration missions to ensure crews have a clean, healthy environment. For info..., visit:
http://www.nasa.gov/home/index.html. For related material on crops and bioengineering, see the Union of Concerned Scientists web page on "Food and Environment"

Summer 2004. Prescription Rice: The Brave New World of Pharma Foods, by Melissa Pamer. Terrain magazine, pp. 10-13. Excerpt: ... Farmers in California's flat, hazy rice fields have worked for years...to please the demanding Japanese palate and gain a toehold in its lucrative market. And it's beginning to work: roughly 40 percent of the rice grown in California goes to Japan. ... Just in the past few years California's rice has finally earned some respect in Japan and other finicky Asian markets, and last year's crop could achieve the best return for farmers in the state's history. But now California farmers worry that the purity of their rice, its hard-won status, and their own livelihood may become casualties of the global debate on genetic modification. At issue is a new kind of rice-a new kind of farm crop, in fact-that is genetically engineered to produce pharmaceuticals. Using the same recombinant DNA techniques that have created GE foods, biotechnology companies are now making plants like rice, corn, and tobacco into "factories" for producing medically useful compounds....Over the past few months, a small Sacramento-based biotechnology company's aim to expand its experimental crop of pharmaceutical rice has caused a shake-up in the normally hermetic California rice industry. In October of last year, Ventria BioScience petitioned the California Rice Commission (CRC) for permission to grow 120 acres of two varieties of rice engineered to produce artificial versions of two human proteins-lysozyme and lactoferrin-which occur naturally in breast milk and tears. ...Ventria's petition set off a review process. ..."One little slip. One slip, that's all it's gonna take. If there's a mistake, the farmer is going to pay-big time," rice farmer Joe Carrancho told the CRC advisory board as it prepared to vote on Ventria's protocol in late March. In work boots and dusty blue overalls, Carrancho held up a chart showing 100 percent opposition to GMO wheat from Japanese consumers. "We are fearful," he said.

 

Articles from 2004–present

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NCSE-National Center for Science Education