科学与翻译

以下是我收集的一些《生物物理》方面参考书，不包括电子版。

Physics and Biology, M.V. Volkenstein (1982)

一本很精炼的概念书，国内有中文版；

生物物理学，赵南明等（2000）

不多的以生物物理为书名的中文书，适合研究生或本科生学习的入门书；

Mathematical Biology, J.D. Murray 2nd edition (1998)

已经是生物数学了，讨论了不少相关数学模型，大多属于微分方程或偏微分方程；

软物质物理学导论，陆坤权等（2006）

书名叫软物质，某些章节属于生物物理方面的，适合相关领域研究生入门阅读；

生物物理学概论，W. 休斯（1979）

这是我从yijun处借来的，一本很老的书，复旦大学译。

亚洲狮是印度的国宝，目前仅在印度的吉尔森林中有300头野生亚洲狮，当然世界各地动物园里还会有不少圈养的。从这一点亚洲狮比华南虎幸运的多，300头可不是个小数字。

这300 头狮子绝大多数生活在1450平方公里的保护区内，是上世纪初由一位印度王子保护的，起初只有12头狮子。这300头狮子的基因是高度趋同的，如果作 DNA鉴定的话，它们就像同卵双胞胎。由于亚洲狮的基因库很小，70%-80%的精子有缺陷，所以300头狮子听起来很多，但它们的前景并不乐观。需要说 明的是狮子处于食物链的最高端，1450平方公里的保护区养活不了300头狮子，最近的调查发现已经有40头狮子从保护区内溜了出来。

与 华南虎事件比较：镇坪县，人口不足7万，总面积1503平方公里，植被覆盖率82.4%，计划建设1000平方公里的自然生态保护区。对群众举报的华南虎 活动频繁的城关镇文彩村、曾家镇向阳村、上竹乡湘坪村、以及钟保镇青林村等四个地带，共150-200平方公里的范围实行特别保护地特别保护措施。从数字 猜测即便这150-200平方公里里面有几只老虎，野生华南虎的前景也不乐观，有时候人的愿望是美好的，但事实终究是事实。

参考：国家地理中文版 2001年 6月号

译自The impact of physics on biology and medicine中的表格，总结得很全面。

A few weeks ago, tiger researchers celebrated the news that a South China tiger (Panthera tigris amoyensis) had been spotted–and photographed–in the wilds of Shannxi Province. But netizens in China and elsewhere have declared it only a “paper tigher” after scrutinizing the two available images.

Although the species has been declared “functionally extinct”, reports of tigher activity in the heavily forested Qinba Mountains prompted Shannxi officials to offer a reward to anyone able to photograph one of the tigers.

At a 12 October press conference in Xian, Zhou Zhenglong, a former hunter, told a rapt audience of his quest to photograph the beast, crawling to within 20 meters of one and snapping 71 images. When the camera’s flash went off, the tiger roared and disappeared, he said.

Skeptics, citing factors such as the tiger’s tame-looking expression and unreal coat color–as well as the fact that the two photos portray exactly the same tiger but differently posotioned foliage–think it’s more likely that some-one planted a cardboard tiger in the bushes. Fu Dezhi, a botanist at the Chinese Academy of Science, adds that the plants are not to scale in relation to the tiger. Zhou, who was paid 20,000 yuan ($2666) for the images, says, “I guarantee with my head that the photographs are authentic.”

The Shannxi Forestry Bureau is pushing ahead with plans for a thorough survey and a tiger reserve. “It’s tremendously exciting nres, if it can be substantiated,” says tiger expert Gary Koehler of Washington state’s Department of Fish and Wildlife(Science, 7 September, p.1312). But first, “they need to look for hair snags or scat” for genetic verification.

(From: Science Vol 318, p.893: 9 Nov 2007 )

转贴：“华南虎事件”《科学》杂志第一次报道原文。

Skilled jade craftsmen may have helped to spread the Austronesian languages. 

Prehistoric purveyors of jade spread their trade from a single Taiwanese source throughout a huge area of Southeast Asia, possibly bringing Austronesian languages with them.

From as early as 3000 BC people from Southeast Asia used jade to make tools and ornaments. This later included ear pendants, such as a three-pointed jade ornament called a lingling-o. These ornaments have been found in southeastern Taiwan, and also all the way out to the Philippines, eastern Malaysia, southern Vietnam, central and southern Thailand, and parts of Cambodia.

Hsiao-Chun Hung, at the Australian National University in Canberra, and her colleagues took a close look at lingling-o and other pendants found in archaeological digs across Southeast Asia, to find out where they came from.

Rather than focus on the style and patterning on the ornaments, Hung used an electron probe microscope, which can work out the elemental composition of each sample without causing any damage. This is the first time that the technique has been used to look at jade, says Hung.

Her work shows that 116 of 144 jade ornaments from across the 3,000-kilometre-wide region came from the Fengtian jade deposit in eastern Taiwan. The Fengtian samples included incomplete ornaments and cast-off pieces of jade thought to come from the manufacturing process, which leads Hung to suggest that the jade was transported as a raw material. “This of course implies movement of people and technology,” says Hung. Her findings are published in Proceedings of the National Academy of Sciences.

Roaming craftsmen

Hung suggests that the raw jade was carried by a few highly proficient, but itinerant, jade workers, who would set up camp and carve it into the lingling-o shapes preferred by the locals.

Finished ornaments were more commonly dated from 500 BC to 500 AD, when there was a flurry in trading activity in the region, and so more chance for a skilled jade worker to travel.

It was already known that obsidian was traded widely across Southeast Asia.

Hung suggests that this trading carried language with it. Today, Austronesian languages are spoken by about 350 million people in Southeast Asia and Oceania. The languages are thought to have started spreading as a people migrated from Taiwan to the Philippines 4,000 years ago. And the distribution of these languages closely mirrors the distribution of Fengtian jade, says Hung.

Fengtian jade and the Austronesian Cham language are both found in southern Vietnam, for example, but not in northern Vietnam — even though northern Vietnam is closer to the Fengtian source.

Nicole Boivin, from the Leverhulme Centre for Human Evolutionary Studies at the University of Cambridge, UK, says that although trade was already widespread in this region at the time in question, using systematic scientific techniques, such as the electron probe microscope, has allowed Hung and her team to get a more detailed picture of what is happening.

“It’s great using scientific methodology to look at this methodically,” says Boivin, “They have really shown in great detail that something is going on.”

References
1. Hung, H.-C. et al. Proc. Nat. Acad. Sci. USA doi 10.1073/pnas.0707304104 (2007).

原文：http://www.nature.com/news/2007/071119/full/news.2007.268.html

A new model of proteins seeks to explain how enzymes extract energy form their vicinity and put it to use in regulating cell chemistry. Enzymes are huge protein molecules that play a crucial role in catalyzing chemical reactions among other molecules or atoms by lowering the energy barrier that would otherwise keep the reaction from happening. Enzymes can therefore be considered as energy-processing chemical-reaction-facilitating machines.

They are usually large, typically containing thousands of heavy (non-hydrogen) atoms, but of these only a few dozen atoms actually participate in the catalytic process. Addressing this important issue, a team of scientists at the Ecole Normale Superieure (Lyon, France) and the Ecole Polytechnique Federale de Lausanne (Switzerland) have concentrated on modeling the behavior of the stiff parts of the enzyme since they believe that some of the energy used in carrying out the catalytic task is stored not just as chemical energy (in the form of adenosine triphosphate, or ATP, the all-purpose “food” of cells) but also as mechanical energy in the form of a waggling or “breathing” motion in the stiffer parts of the enzyme.

Extending this research to proteins in general, Yves-Henri Sanejouand says that he and his colleagues would like to scrutinize in more detail the nonlinear process by which some proteins catch and store thermal energy from their environment and also how chemical energy can be turned into mechanical energy, such as in muscle contraction.

原文：http://www.aip.org/pnu/2007/split/846-2.html

It seems unlikely that a toddler would pass up a teddy bear for a hunk of metal. But in a new study, toddlers developed strong social bonds with robots, largely ignoring their traditional toys. The findings represent a step forward in human-robot interactions.People’s bonds with their pets tend to strengthen over time, but most available robots geared toward interacting with people, such as Sony’s mechanical puppy AIBO, have tended to lose their appeal within about 10 hours. Eager to break the so-called 10-hour barrier, Fumihide Tanaka, a robotics researcher at the University of California, San Diego (UCSD), and colleagues tested the Sony QRIO, a state-of-the-art humanoid robot that can recognize faces and respond to touch.

The researchers chose toddlers for the tests because they “have no preconceived notions of robots,” Tanaka says. Children at UCSD’s daycare facility interacted with QRIO for 45 sessions averaging 50 minutes each over 5 months. The sessions were videotaped, and student volunteers evaluated the closeness of the interactions. The team also gauged the children’s “haptic contact”–how much and where they touched the robot–and compared it with how they treated toys and other children.

During the first 27 sessions, the robot was responsive to the children, giggling when its head was touched. The children enjoyed interacting with the robot during this period, the team reports.

The researchers then restricted QRIO’s behavior to a more predictable, nonresponsive dance routine for 15 sessions, and children’s interest declined. At the end of the study, the team reinstated its full repertoire for three sessions, and interest picked up. Programming the robot to respond to the children was key to engaging them, the team reports online 5 November in the Proceedings of the National Academy of Sciences.

The children also came to prefer hugging QRIO more than they preferred hugging a teddy bear or an inanimate robot doll, and they touched QRIO carefully, in the same way that they touched other children, rather than bashing it as they did the doll.

Even though he sent a command to the robot about once every 2 minutes, Tanaka says “the results imply that current robot technology is surprisingly close to achieving [sustained] autonomous bonding and socialization with human toddlers.”

Other experts are more cautious. “The authors are drawing general conclusions … beyond what the data alone suggest,” says Nathan Freier, a technologist and social scientist at Rensselaer Polytechnic Institute in Troy, New York. According to Freier, “haptic contact …cannot stand alone as an indicator of bonding or socialization.” But he calls the study an “excellent foundation” for future studies into childhood development and technology design.

原文：http://sciencenow.sciencemag.org/cgi/content/full/2007/1105/2

Autumn leaves turn fiery-red in an attempt to store up as much goodness as possible from leaves and soil before a tree settles down for the winter. The worse the quality of soil, the more effort a tree will put in to recovering nutrients from its leaves, and the redder they get.

That’s the conclusion that Emily Habinck from the University of North Carolina, Charlotte, came to after looking at trees in a flood plain and in an adjacent upland area. The soil in the upland area was low in nutrients, and the leaves there were bright red. In the floodplain, where the soil was packed full of goodness, the autumn leaves remained yellow.

“In a nutshell: the redder a leaf is, the more nutrients it is going to recycle,” explains Habinck, who presents her findings at the Geological Society of America’s annual meeting in Denver, Colorado, today.

It’s not easy being red

Unlikely as it may seem, colour changes in leaves are not fully understood — at least not when it comes to the redder hues.

As autumn approaches, trees begin to break down the green chlorophyll in their leaves and redistribute the nutrients contained there to their trunk and roots. This keeps them going throughout the winter, when sunlight is sparse.

The yellow colour seen in some autumn trees results from the loss of chlorophyll simply unmasking the yellow carotinoids that were there all along. But red coloration comes from a nitrogen-containing pigment called anthocyanin, which has to be made afresh as autumn takes hold.

Why trees would bother to spend energy doing this as things are winding down for the winter has been widely debated. Some researchers have suggested that these pigments act as antioxidants, which help a tree combat harsh conditions. Others say it helps to attract birds that can then disperse fruits. Or it might increase leaf temperature, helping to protect from the cold.

Sunscreen

Some people have observed that trees tend to turn redder when an autumn is particularly bright and cold. In 2001, William Hoch, now at Montana State University, Bozeman, suggested that the pigment acts as a protective sunscreen, helping to keep leaves on the trees for longer so that more nutrients can be harvested from them. Photosynthesis becomes more difficult as chlorophyll is broken down, and leaves become more susceptible to damage from the Sun. Damaged leaves will fall more quickly, and rid the tree of a nutrient supply.

Hoch did a study in which he made mutant trees that couldn’t produce anthocyanins. These dropped their leaves while they were still green when exposed to the high-stress environment of bright light and cold temperatures. The mutant trees were much less efficient at storing up nitrogen for the winter.

Habinck’s study of natural sweetgum and red maple trees in a nature preserve in Charlotte supports this notion. Trees in the upland areas, where soils don’t have much nitrogen, had much redder leaves than the trees in the flood-plain environment.

“A plant on a nutrient-poor soil is going to be more concerned about keeping the nutrients it has,” says Hoch. So it will turn red to stop its leaves dropping prematurely.

Habinck’s supervisor, Martha Eppes, now wants to look at satellite data to see whether there is a wider correlation between tree colour and soil type over large areas.

原文：http://www.nature.com/news/2007/071029/full/news.2007.202.html

The gift of gab sets humans apart from all other species. But what about Neandertals? A new genetic study offers tantalizing evidence that our closest extinct cousins may have been talkative, too.Nailing down whether Neandertals spoke to each other has been tricky. Studies show that they had big brains and engaged in some sophisticated behaviors, including burying their dead. But the evidence has been indirect because the soft structures of the throat don’t fossilize, and researchers have debated whether they could speak as well as we do. Recent work on a gene known as FOXP2 seems to undermine the speaking hypothesis. Many animals, including mice and bats, have the gene, but specific variations in the human version appear to have contributed to our language ability. Research indicates that these variations appeared in the past 120,000 years–long after our species split from Neandertals. “So the speculation was that [the FOXP2 variations] were unique to humans and not there in Neandertals,” says evolutionary geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who traced FOXP2’s ancestry. “If there was one single gene I really wanted to see in Neandertals, it was this one.”

Pääbo appears to have gotten his wish: His team extracted ancient DNA from two 43,000-year-old Neandertal bones found in a cave in northern Spain. Genetic analysis revealed that the FOXP2 sequence in both Neandertals matched that in living people. It harbored the two mutations that help set the human gene apart from those of all other animals. This doesn’t necessarily prove that Neandertals could speak, because many other, unknown genes probably influence language ability. But “with respect to FOXP2, there’s nothing to say that Neandertals could not speak just like we do,” says Pääbo. He now suggests that the gene was favored by selection much earlier, before Neandertals and modern humans had completely diverged, perhaps 300,000 or 400,000 years ago. The team reports its findings online 18 October in Current Biology.

Several experts say that vocal Neandertals fit what we know of these hominids, especially the fact that they had large brains and lived in groups. “I think many of us are prepared to grant Neandertals language capacity, even if … it may not have reached our modern levels,” says Chris Stringer of the Natural History Museum in London. Still, evolutionary geneticist Jeff Wall of the University of California, San Francisco, cautions that it’s possible that the Neandertal samples were contaminated with modern human DNA. Pääbo says that for this paper, the team added extra controls to try to make sure that they were analyzing Neandertal rather than modern human DNA.

Even if there were no contamination, Wall says, it’s not clear exactly when Neandertals acquired the humanlike FOXP2 gene and its potential effect on speech. Instead of belonging to a common ancestor of both species, Wall says it’s possible that the study’s Neandertals, who lived in Europe just as modern humans were beginning to enter the continent, picked up the FOXP2 variant by mixing with the newcomers. Pääbo calls that scenario “a formal possibility but one we think unlikely.”

原文网址：http://sciencenow.sciencemag.org/cgi/content/full/2007/1018/3

By exploiting millions of hours of computing time donated by the users of 150,000 home computers, scientists have predicted the structure of a protein using just its sequence of amino acids. The project marks a significant advance in a field that’s been flush with hope yet short on tangible results, experts say.

Determining the shape of a protein is normally a matter of firing X-ray beams at its crystalline form and measuring their diffraction, and protein chemists have long been sceptical of attempts to replace this practice with modelling or theory. “Modelling right now has a terrible name in the field,” says Michael Levitt, a computational biologist at Stanford University. But in a Nature paper published online on 14 October, David Baker, a biochemist at the University of Washington in Seattle, and his colleagues report results that may do much to dispel that scepticism (B. Qian et al. Nature doi:10.1038/nature06249; 2007).

A protein’s shape — and therefore its activity — is determined by the precise way its constituent string of amino acids folds up. “If you think of the whole thing as like an utterly flexible snake, there are hundreds of degrees of freedom at every site,” says Eleanor Dodson, a structural biologist at the University of York, UK. The final shape depends on the molecular interactions each amino acid has with its neighbours, with surrounding water molecules and with other amino acids that are a long distance away in terms of sequence, but which become close as a result of folding. It’s a horrendous problem to model.

Rather than trying to solve the problem from first principles, Baker’s technique combines information from the sum of what is already known about protein structures with the vast computing power available through the Berkeley Open Infrastructure for Network Computing. This software, developed at the University of California, Berkeley, allows people to contribute spare computing power on their desktops to scientific projects (most famously, the search for extraterrestrial intelligence, in the form of SETI@home); 150,000 volunteers used it to download a copy of the Baker lab’s Rosetta@home program.

Rosetta breaks a protein’s sequence into short stretches that can be matched to identical stretches from proteins with known structures. These shapes offer many ways to sew the protein under study back together, and the program chooses those that minimize the free energy of the structure (a measure of its stability). By running the program over and over again on thousands of computers, the researchers lurched towards an ever more accurate protein model.

When fed the sequence of T0283, a 112-amino-acid protein from a bacterium, the network spat out several million structures after a million hours of computing time. Those millions were whittled down to five by further repeated computer analysis, and one of the structures was spot on, correlating with the structure as determined from its crystal.

Although the structure’s precision was not on a par with high-resolution crystal models, it was good enough for researchers to think that the technique could simplify the process of obtaining X-ray structures in the future. To turn X-ray patterns into structures, researchers must produce patterns from crystals that have either been spiked with heavy-metal ‘markers’ or come with some indication of what the final structure will look like, for example from the shape of a related protein. Rosetta’s structure for T0283 was good enough to function in this way. The program should now be able to provide such reference points for proteins for which there are already X-ray data, but which lack useful relatives and whose structures thus languish unsolved. “You will be able to solve a whole bunch of these structures rather quickly,” says Adrian Roitberg, a protein modeller at the University of Florida in Gainesville.

There is still room for improvement, though, says Rhiju Das, a postdoc working on the Rosetta@home project and a co-author on Baker’s paper. Each home computer works in isolation, he explains. If the program could be rewritten to run on the many parallel processors in a supercomputer, Rosetta might become considerably more powerful.

One pay-off of better structure prediction would be the prospect of custom-made proteins, says Baker, who uses Rosetta to hunt for sequences that correspond to desired structures. His lab and that of University of Washington biochemist Bill Schief are currently working on redesigning the gp120 protein of HIV to make a vaccine that could stimulate the immune system in a different way from the natural virus. The reshaped protein should elicit antibodies that attack the virus more effectively than antibodies created after infection.

The days when protein modellers thought they could make crystallization obsolete are long gone, Baker adds. But melding the two techniques could offer biologists insight into many more proteins — and faster. “If you really care about the structure of your protein, you should get some experimental data and combine it with modelling,” he says.

原文网址 http://www.nature.com/news/2007/071016/full/449765a.html