Published: June 29, 2007

Scientists at the institute directed by J. Craig Venter, a pioneer in sequencing the human genome, are reporting that they have successfully transplanted the genome of one species of bacteria into another, an achievement they see as a major step toward creating synthetic forms of life.

Other scientists who did not participate in the research praised the achievement, published yesterday on the Web site of the journal Science. But some expressed skepticism that it was as significant as Dr. Venter said.

His goal is to make cells that might take carbon dioxide out of the atmosphere and produce methane, used as a feedstock for other fuels. Such an achievement might reduce dependency on fossil fuels and strike a blow at global warming.

“We look forward to having the first fuels from synthetic biology certainly within the decade and possibly in half that time,” he said.

Richard Ebright, a molecular biologist at Rutgers University, said the transplantation technique, which leads to the transferred genome’s taking over the host cell, was “a landmark accomplishment.”

“It represents the complete reprogramming of an organism using only a chemical entity,” Dr. Ebright said.

Leroy Hood, a pioneer of the closely related field of systems biology, said Dr. Venter’s report was “a really marvelous kind of technical feat” but just one of a long series of steps required before synthetic chromosomes could be put to use in living cells.

“It’s a really worthy accomplishment, but I hope it doesn’t get hyped to be more than it is,” Dr. Hood said.

One reason for Dr. Venter’s optimism is that he says his institute is close to synthesizing from simple chemicals an entire genome, 580,000 DNA units in length, of a small bacterium, Mycoplasma genitalium. If that genome can be made to take over a bacterium using the method announced today, Dr. Venter should be able to claim that he has made the first synthetic life form. The bacterium would be identical to nature’s version, but would demonstrate how precise control could be achieved over every aspect of the machinery of living cells.

Biologists have long been able to move useful genes into bacteria and other organisms in a process called genetic engineering. The idea of synthetic biology is to carry out genetic engineering in a more extensive and systematic way.

Synthetic biologists, who held their third annual meeting in Zurich, Switzerland, this week, hope to create biochemical processes and then choose the gene sequences that will direct these processes and build the DNA from scratch. The scientists’ goal is to select and reorder the genetic machinery developed by evolution just as an engineer might assemble an efficient circuit board from existing components.

Dr. Venter hopes to lay the basis for a new approach to synthetic biology by first synthesizing whole genomes in the laboratory and then making them take control of, or “boot up,” a living cell. His new report accomplishes the second of the two steps, at least in Mycoplasma. His team, which includes a distinguished biologist, Hamilton Smith, purified the full DNA from one kind of Mycoplasma and showed that it could take control of another, making the host cell switch over to producing proteins specified by the inserted DNA. Dr. Smith said he was not sure whether the inserted genome destroyed the host genome or just made the cell divide, assigning the two genomes to different daughter cells.

Booting up cells with new genomes is a major limitation in synthetic biology, Dr. Venter said. With that hurdle now crossed, it will be possible to “design cells in future to manufacture new types of fuel and break our dependency on oil and do something about carbon dioxide going into the atmosphere.”

Dr. Hood, co-founder of the Institute for Systems Biology in Seattle, said the next step on Dr. Venter’s agenda, putting a functional synthetic genome into an organism, would be more significant.

“Synthesizing a whole chromosome and getting it to function will be a really remarkable step that will be much closer to the golden vision of creating new organisms,” he said.

The longest piece of DNA synthesized so far, he explained, is 35,000 units long, whereas the Mycoplasma genome or chromosome is 580,000 units.

The synthetic Mycoplasma, if the Venter team is successful, would be identical to the natural kind and should present no conceivable hazard. But synthetic biology is a technique with potentially far-reaching consequences like environmental effects and misappropriation by terrorists. In addition, the ability to synthesize living organisms may provoke philosophical comment.

Scientists have taken the initiative in assessing the effects with the hope of staying far enough ahead of events to avoid regulation. A report on the possible dangers of synthetic biology is being prepared for the Sloan Foundation by scientists at M.I.T., the Venter Institute and the Center for Strategic and International Studies.



六月 29, 2007

Lindsay Mangum

The Keeling Curve is named after Charles David Keeling, the first scientist to report that global atmospheric concentrations of carbon dioxide were rising. From the observatory atop Mauna Loa, Hawaii, Keeling began the first continuous record of global carbon dioxide in 1958. Oscillations in the curve represent seasonal fluctuations in carbon dioxide levels. NPR

Lindsay Mangum

 Measurements of temperatures over the course of the 20th century show the planet, on average, has warmed by 1 degree Celsius. Temperature-change computer simulations only match up with observed temperatures if human activity, e.g. burning fossil fuels, is taken into account. The blue-shaded band, based on simulations that only take into account natural systems, such changes in the sun’s output or volcanic eruption, falls short of the temperature change actually observed. NPR

(Note: Green color band stands for computer prediction of temperature change, without fossil fuel use)

Lindsay Mangum

The long-term record of atmospheric carbon dioxide obtained from Antarctic ice cores shows huge fluctuations over the past 150,000 years. Periods of low carbon dioxide concentration correspond to ice ages, while higher carbon dioxide concentrations are linked to warmer periods. NPR

(Note: Scientists studying air bubbles trapped in ice cores have found that over the last 650,000 years, CO2 levels in the atmosphere ranged from about 180 parts per million (ppm) to 300 ppm. Just prior to Britain’s Industrial Revolution, levels hovered at 280 ppm, according to the latest report from the United Nation’s Intergovernmental Panel on Climate Change. CO2 levels had risen to 379 ppm by 2005, and are increasing at an average of nearly 2 ppm per year.

The trend is pretty similar for other major greenhouse gases produced by human activities. Methane concentrations have more than doubled from 715 parts per billion (ppb) in pre-industrial times to 1774 ppb in 2005. And nitrous oxide levels have spiraled from 270 ppb to 319 ppb.)

nucifera 注: 这几个图表在Al Gore的《An Inconvenient Truth》中有更清楚地说明和解释。在这几张图表背后有好些意味,Al Gore作为演说家也非常清楚地对此作出讲解。

Published: June 28, 2007

There may be a silver lining in the recent hedge fund debacle at Bear Stearns.

Until now, the deepest pain of the housing slump has been felt by hard-pressed borrowers, generally low-income homeowners stuck with unsuitable and even predatory subprime loans — adjustable-rate mortgages made to people with weak credit. As monthly payments have increased, the loans have become unaffordable, while falling housing prices and tougher credit terms have made them harder to refinance. Defaults and foreclosures have multiplied, but Congress has provided scant relief.

But now the pain is being felt by Wall Street. The two big Bear Stearns hedge funds that neared collapse last week were full of tricky investments tied to subprime mortgages. To try to ensure that hundreds of billions of dollars worth of similar investments don’t also plummet, endangering the financial system, Congress may finally have to do more to help lower-end borrowers. That, in turn, would prop up the investments based on their mortgages.

We’re all for helping distressed borrowers. And we accept government’s role, if necessary, to avert a financial collapse. But in the end, intervention on behalf of Wall Street would be an outrage, because Wall Street — abetted by lax federal regulation — is largely to blame for this fiasco. Wall Street firms encouraged the issuance of risky loans to troubled borrowers and then reaped a windfall by packaging them as investments for hedge fund clients.

And yet, the possibility of economywide problems from further Bear Stearns-like debacles is real. The Bear Stearns funds, like many others, borrowed big to invest in subprime loans. Investing with borrowed money juices returns in hot markets and magnifies losses in down markets, making losers out of lenders as well as equity investors.

One of the Bear Stearns funds borrowed some $6 billion, from Merrill Lynch, Goldman Sachs, Bank of America and other powerhouses. For the other fund, Bear Stearns reportedly put up $3.2 billion to help liquidate holdings. That’s 32 cents on the dollar for assets once valued at $10 billion.

In the past two years, Wall Street firms have issued investments similar to the Bear Stearns holdings, worth about $500 billion on paper. If those were to tank, the damage could be felt broadly. It would likely become harder, for instance, to get loans for everything from homebuying, which supported the economy for most of the decade, to leveraged buyouts, which have buoyed the stock market.

It should not be permitted for lenders, banks and hedge funds to risk everyone’s economic well-being in their attempts to enrich the few. The country needs vastly better regulation than it now has. Mortgage lenders must be restricted to recommending loans that are reasonably within the borrowers’ ability to repay over time. Federal bank regulation must be streamlined and toughened to avoid a repeat of the disjointed and ultimately lax response to the reckless lending of the housing boom.

Hedge funds should be regulated if they accept pension money, because doing so exposes everyday Americans to outsized investment risks. Regulation should also cover hedge funds with large sums of borrowed money. And the United States must embrace global coordination of hedge fund regulation, just as banking regulation is increasingly global.

In the coming year, interest rates on some $850 billion in mortgages are scheduled for their first increase. Over half of that is in subprime loans. That is the dangerous financial world we live in. It needs strong regulations.


Published: June 27, 2007

SINGAPORE, June 26 — Under the sink, behind the cleaning detergents, Thurainadan Govindarajoo shined his flashlight into the shadows, searching for telltale signs of the enemy.

“People only think of the obvious places,” he said. “We’re looking for what I call the hidden habitats.” Under leaking sinks, in disused toilets, beneath potted plants: wherever a few drops of water can linger, mosquitoes can breed.

Mr. Govindarajoo is one of roughly 500 inspectors from Singapore’s National Environment Agency specially trained to conduct house-to-house search-and-destroy missions against Aedes mosquitoes, which transmit the potentially deadly dengue virus. Despite their best efforts, though, the mosquitoes appear to be winning, abetted by the boom in international travel, global warming and their own adaptability.

Singapore and its Southeast Asian neighbors are in the midst of a new epidemic of dengue (pronounced DEN-gay) that is already on course to claim more victims regionally than the last epidemic, in 2005.

Thailand has already had more than 11,000 reported cases so far this year, with 14 deaths, while 48 people have died among Malaysia’s more than 20,000 dengue cases. Sprawling Indonesia, with more than 68,000 reported cases, has had 748 deaths. And while Singapore’s two dengue-related deaths give it the lowest fatality rate in the region, its nearly 3,000 cases make its infection rate second only to Malaysia’s.

Dengue is a relative of yellow fever, hepatitis C and the West Nile virus. It infects an estimated 50 million people a year, and there remains no vaccine or treatment. In acute cases, it causes high fever and debilitating lethargy, accompanied by joint pain so intense that the disease was called “breakbone fever” when it was first diagnosed more than 300 years ago. About 1 percent of these more serious cases develop hemorrhagic fever or shock, with gastrointestinal bleeding and, in rare cases, brain hemorrhages and death.

Although there are incidences of dengue around the year in tropical climates, cases tend to spike during periods of high rainfall and high temperatures.

If there is a silver lining to Singapore’s dengue problem, it is that it has turned the island state into a global center for knowledge about the disease. As Singapore has promoted itself as a hub for biotechnology research, dengue has quickly become a common cause. In 2004, for example, the pharmaceutical company Novartis opened an Institute for Tropical Disease here, with a specific focus on developing a treatment for dengue.

Nonetheless, results have been slow in coming. “There’s no quick fix here,” said Paul Herrling, head of corporate research at Novartis.

Dengue is an enigmatic virus, difficult to diagnose and impossible to quarantine. Ninety percent of those infected with dengue develop only mild flulike symptoms, if they feel anything at all, making them unwitting reservoirs for the virus.

Even when symptoms appear, they do so days after the patient has become infectious. And after the onset of dengue’s characteristic fever that varies widely in temperature, antibodies do not appear in significant levels for days, meaning doctors cannot use conventional blood tests to detect the virus until the worst is already over.

Creating a vaccine against dengue might be a simple matter if it were not for another quirk of the virus. Dengue has four known strains, and while infection with one strain appears to provide lifelong immunity against that strain and one of the others, it seems to make a person more likely to hemorrhage if infected with one of the other two strains. Any vaccine, therefore, would have to work simultaneously against all four strains.

Because dengue was long confined to the tropics, it remains a little-understood disease. Experts still do not know precisely how the virus affects the liver or why it causes the level of blood-clotting platelets in the bloodstream to decline.

The virus is spreading fast. Global warming is extending the Aedes mosquitoes’ habitat so that dengue has now marched north from Latin America to the southern United States. Commercial aviation is also carrying infected individuals — and Aedes mosquitoes — to new areas.

If the virus cannot be blocked or the people carrying it detected and quarantined, the only logical alternative is to thwart the mosquito that transmits it. Singapore’s mosquito control program is widely recognized as the world’s most rigorous. There are widespread public awareness campaigns. Posters around the island now picture a black-and-white-striped, blood-engorged Aedes with a warning: “If they breed, you will bleed.”

Doctors here are required by law to report dengue cases to the Ministry of Health, which sends the information daily to the National Environment Agency. At the agency, the cases are plotted on an islandwide map in a dedicated dengue situation room. Any area where two cases occur within 14 days of each other in a 150-meter radius is designated a hot spot, and inspectors like Mr. Govindarajoo are dispatched to scour the area for mosquito breeding sites.

The inspectors called to the Indonesian maid at a house in Lengkong, a neighborhood where seven dengue cases had erupted in recent weeks: “Hello. Good morning. Selamat pagi. Checking for mosquitoes.”

The inspectors fanned out, some climbing ladders to check gutters, while others searched the garden for standing water in potted plants or between the leaves of palm trees.

Aedes aegypti, the most prolific transmitter of dengue, has become ideally suited to the rapidly growing tropical urban environment. Unlike malaria-transmitting mosquitoes that stick to rural areas and swampy waters, it prefers fresh, clean water. It breeds largely indoors, needing only tiny pools of water to lay its eggs. Christina Liew, a medical entomologist at the agency, said Aedes mosquitoes are not as fussy about where they will lay eggs as was once believed. In the absence of clean water, Ms. Liew said, females will lay eggs in polluted water.

“They have learned to adapt to urban situations,” she said.


六月 27, 2007




或许是我过于斤斤计较,戴起高帽摆起专家的大样子。不过这种缥缈口号喊得多了,巴普洛夫(Ivan Pavlov)的classical conditioning作用就会异常有效。凡是专搞品牌效应的生意人对此都很有一手。这种效应被滥用后最直接的结果,就是让人有对事物有错误的印象。


巴普洛夫就是那个吃饱撑着的生物学家,那狗儿的反应就叫classical conditioning。





Published: June 26, 2007

In 1950, in a letter to bishops, Pope Pius XII took up the issue of evolution. The Roman Catholic Church does not necessarily object to the study of evolution as far as it relates to physical traits, he wrote in the encyclical, Humani Generis.” But he added, “Catholic faith obliges us to hold that souls are immediately created by God.”

Pope John Paul II made much the same point in 1996, in a message to the Pontifical Academy of Sciences, an advisory group to the Vatican. Although he noted that in the intervening years evolution had become “more than a hypothesis,” he added that considering the mind as emerging merely from physical phenomena was “incompatible with the truth about man.”

But as evolutionary biologists and cognitive neuroscientists peer ever deeper into the brain, they are discovering more and more genes, brain structures and other physical correlates to feelings like empathy, disgust and joy. That is, they are discovering physical bases for the feelings from which moral sense emerges — not just in people but in other animals as well.

The result is perhaps the strongest challenge yet to the worldview summed up by Descartes, the 17th-century philosopher who divided the creatures of the world between humanity and everything else. As biologists turn up evidence that animals can exhibit emotions and patterns of cognition once thought of as strictly human, Descartes’s dictum, “I think, therefore I am,” loses its force.

For many scientists, the evidence that moral reasoning is a result of physical traits that evolve along with everything else is just more evidence against the existence of the soul, or of a God to imbue humans with souls. For many believers, particularly in the United States, the findings show the error, even wickedness, of viewing the world in strictly material terms. And they provide for theologians a growing impetus to reconcile the existence of the soul with the growing evidence that humans are not, physically or even mentally, in a class by themselves.

The idea that human minds are the product of evolution is “unassailable fact,” the journal Nature said this month in an editorial on new findings on the physical basis of moral thought. A headline on the editorial drove the point home: “With all deference to the sensibilities of religious people, the idea that man was created in the image of God can surely be put aside.”

Or as V. S. Ramachandran, a brain scientist at the University of California, San Diego, put it in an interview, there may be soul in the sense of “the universal spirit of the cosmos,” but the soul as it is usually spoken of, “an immaterial spirit that occupies individual brains and that only evolved in humans — all that is complete nonsense.” Belief in that kind of soul “is basically superstition,” he said.

For people like the evolutionary biologist Richard Dawkins, talk of the soul is of a piece with the rest of the palaver of religious faith, which he has likened to a disease. And among evolutionary psychologists, religious faith is nothing but an evolutionary artifact, a predilection that evolved because shared belief increased group solidarity and other traits that contribute to survival and reproduction.

Nevertheless, the idea of a divinely inspired soul will not be put aside. To cite just one example, when 10 Republican presidential candidates were asked at a debate last month if there was anyone among them who did not believe in evolution, 3 raised their hands. One of them, Senator Sam Brownback of Kansas, explained later in an op-ed article in this newspaper that he did not reject all evolutionary theory. But he added, “Man was not an accident and reflects an image and likeness unique in the created order.”

That is the nub of the issue, according to Nancey Murphy, a philosopher at Fuller Theological Seminary who has written widely on science, religion and the soul. Challenges to the uniqueness of humanity in creation are just as alarming as the Copernican assertion that Earth is not the center of the universe, she writes in her book “Bodies and Souls or Spirited Bodies?” (Cambridge, 2006). Just as Copernicus knocked Earth off its celestial pedestal, she said, the new findings on cognition have displaced people from their “strategic location” in creation.

Another theologian who has written widely on the issue, John F. Haught of Georgetown University, said in an interview that “for many Americans the only way to preserve the discontinuity that’s implied in the notion of a soul, a distinct soul, is to deny evolution,” which he said was “unfortunate.”

There is no credible scientific challenge to the theory of evolution as an explanation for the diversity and complexity of life on earth.

For Dr. Murphy and Dr. Haught, though, people make a mistake when they assume that people can be “ensouled” only if other creatures are soulless.“

Evolutionary biology shows the transition from animal to human to be too gradual to make sense of the idea that we humans have souls while animals do not,” wrote Dr. Murphy, an ordained minister in the Church of the Brethren. “All the human capacities once attributed to the mind or soul are now being fruitfully studied as brain processes — or, more accurately, I should say, processes involving the brain, the rest of the nervous system and other bodily systems, all interacting with the socio-cultural world.”

Therefore, she writes, it is “faulty” reasoning to want to distinguish people from the rest of creation. She and Dr. Haught cite the ideas of Thomas Aquinas, the 13th-century philosopher and theologian who, Dr. Haught said, “spoke of a vegetative and animal soul along with the human soul.”

Dr. Haught, who testified for the American Civil Liberties Union when it successfully challenged the teaching of intelligent design, an ideological cousin of creationism, in the science classrooms of Dover, Pa., said, “The way I look at it, instead of eliminating the notion of a human soul in order to make us humans fit seamlessly into the rest of nature, it’s wiser to recognize that there is something analogous to soul in all living beings.”

Does this mean, say, that Australopithecus afarensis, the proto-human famously exemplified by the fossil skeleton known as Lucy, had a soul? He paused and then said: “I think so, yes. I think all of our hominid ancestors were ensouled in some way, but that does not rule out the possibility that as evolution continues, the shape of the soul can vary just as it does from individual to individual.

”Will this idea catch on? “It’s not something you hear in the suburban pulpit,” said Dr. Haught, a Roman Catholic whose book “God After Darwin” (Westview Press, 2000) is being reissued this year. “This is out of vogue in the modern world because the philosopher Descartes made such a distinction between mind and matter. He placed the whole animal world on the side of matter, which is essentially mindless.”

Dr. Haught said it could be difficult to discuss the soul and evolution because it was one of many issues in which philosophical thinking was not keeping up with fast-moving science. “The theology itself is still in process,” he said.

For scientists who are people of faith, like Kenneth R. Miller, a biologist at Brown University, asking about the science of the soul is pointless, in a way, because it is not a subject science can address. “It is not physical and investigateable in the world of science,” he said.“

Everything we know about the biological sciences says that life is a phenomenon of physics and chemistry, and therefore the notion of some sort of spirit to animate it and give the flesh a life really doesn’t fit with modern science,” said Dr. Miller, a Roman Catholic whose book, “Finding Darwin’s God” (Harper, 1999) explains his reconciliation of the theory of evolution with religious faith. “However, if you regard the soul as something else, as you might, say, the spiritual reflection of your individuality as a human being, then the theology of the soul it seems to me is on firm ground.”

Dr. Miller, who also testified in the Dover case, said he spoke often at college campuses and elsewhere and was regularly asked, “What do you say as a scientist about the soul?” His answer, he said, is always the same: “As a scientist, I have nothing to say about the soul. It’s not a scientific idea.”