Technology Trends

In “Life on the Scales,” Science News recently wrote that some simple mathematical equations, known as quarter-power scaling laws, can explain the metabolic rates of living organisms. For example, “an animal’s metabolic rate appears to be proportional to mass to the 3/4 power.” And this “3/4-power law appears to hold sway from microbes to whales, creatures of sizes ranging over a mind-boggling 21 orders of magnitude.” The ecologists, physicists and chemists behind this research are now successfully applying this equation to plants, fish, full ecosystems and even biology and genetics, by adding a new key parameter: temperature. Please read this fascinating article for many more details and references. But save some time to read another long article, “Ecology’s Big, Hot Idea,” published by PLoS Biology, which states that “the way life uses energy is a unifying principle for ecology in the same way that genetics underpins evolutionary biology.” Read more…

The Science News article starts with a simple observation. Although a mouse has a shorter life than an elephant, both clock approximately the same number of heartbeats during their lives. Simply, their metabolisms are different. Now, let’s go back several decades ago.

Scientists have long known that most biological rates appear to bear a simple mathematical relationship to an animal’s size: They are proportional to the animal’s mass raised to a power that is a multiple of 1/4. These relationships are known as quarter-power scaling laws. For instance, an animal’s metabolic rate appears to be proportional to mass to the 3/4 power, and its heart rate is proportional to mass to the –1/4 power.

In subsequent decades, biologists have found that the 3/4-power law appears to hold sway from microbes to whales, creatures of sizes ranging over a mind-boggling 21 orders of magnitude.

But nobody had an explanation for this scaling law – until 1997.

The beginnings of an explanation came in 1997, when ecologist James Brown of the University of New Mexico in Albuquerque, physicist Geoffrey West of Los Alamos (N.M.) National Laboratory, and Brian Enquist, an ecologist at the University of Arizona in Tucson, described metabolic scaling in mammals and birds in terms of the geometry of their circulatory systems. It turns out, West says, that Rubner was on the right track in comparing surface area with volume, but that an animal’s metabolic rate is determined not by how efficiently it dissipates heat through its skin but by how efficiently it delivers fuel to its cells.

The idea, West says, is that a space-filling surface scales as if it were a volume, not an area. If you double each of the dimensions of your laundry machine, he observes, then the amount of linens you can fit into it scales up by 2³, not 2². Thus, an animal’s effective surface area scales as if it were a three-dimensional, not a two-dimensional, structure.

This law also can be applied to plants, fish, or even cancer growth rates — providing you add a new parameter: temperature.

In 2001, after James Gillooly, a specialist in body temperature, joined Brown at the University of New Mexico, the researchers and their collaborators presented their master equation, which incorporates the effects of size and temperature. An organism’s metabolism, they proposed, is proportional to its mass to the 3/4 power times a function in which body temperature appears in the exponent.

When the researchers filter out the effects of body temperature, most species adhere closely to quarter-power laws for a wide range of properties, including not only life span but also population growth rates. The team is now applying its master equation to more life processes — such as cancer growth rates and the amount of time animals sleep.

Now, it’s time for two key quotes [which don't appear in bold characters in the original article.]

“We’ve found that despite the incredible diversity of life, from a tomato plant to an amoeba to a salmon, once you correct for size and temperature, many of these rates and times are remarkably similar,” says Gillooly.

“Metabolic rate is, in our view, the fundamental biological rate,” Gillooly says. There is a universal biological clock, he says, “but it ticks in units of energy, not units of time.”

Then the researchers applied their master equation to ecosystems such as forests, and even to evolutionary biology, trying to answer this question: “Why do the fossil record and genetic data often give different estimates of when certain species diverged?”

When the researchers use their master equation to correct for the effects of size and temperature, the genetic estimates of divergence times — including those of rats and mice — line up well with the fossil record, says Allen, one of the paper’s coauthors.

As I wrote in the introduction, don’t miss this other paper by John Whitfield in PLoS Biology on a similar subject, “Ecology’s Big, Hot Idea.” Here are the two first paragraphs.

Life is complicated. It comes in all sorts of shapes, sizes, places, and combinations, and has evolved a dizzying variety of solutions to the problem of carrying on living. Yet look inside a cell and life takes on, if not simplicity, then at least a certain uniformity — a genetic system based around nucleic acids, for example, and a common set of chemical reactions for turning food into fuel. And looked at in broad swathes, life shows striking generalities and patterns. Every mammal’s heart will beat about one billion times in its lifetime. Both within and between species, the density of a population declines in a regular way as the size of individuals increases. And the number of species in all environments declines as you move from the equator towards the poles.

Wouldn’t it be good if there were a simple theory that used life’s shared fundamentals to explain its large-scale regularities, via its diversity of individuals? In the past few years, a team of ecologists and physicists have come up with just such a theory. At its heart is metabolism: the way life uses energy is, they claim, a unifying principle for ecology in the same way that genetics underpins evolutionary biology. They believe that energy use, in the form of metabolic rate, can be understood from the first principles of physics, and that metabolic rate can explain growth, development, population dynamics, molecular evolution, the flux of chemicals through the environment, and patterns of species diversity — to name a few.

If you don’t have enough time today, print the two articles I mentioned and read them next weekend. I promise you will not waste your time.

Sources: Erica Klarreich, Science News, Vol. 167, No. 7, p. 106, February 12, 2005; John Whitfield, PLoS Biology, Vol. 2, Issue 12, December 14, 2004

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Researchers at the University of California, Davis, have recorded the behavior of baby rats in enclosed rectangular environments and saw that the rat pups, almost blind and deaf, didn’t move much after hitting the walls of their cages. They decided to build rat-like robots, inject them some software and rules, and see what will come from this. Surprisingly, they saw that their robots didn’t follow their software rules and started unexpected movements, such as circling the rectangular arena after a shock into a wall. This led them to revisit the original animal data and to conclude that baby rats also had similar behaviors even if they didn’t pay attention to it previously. Now the researchers want to give different sets of rules to their rat-like robots to predict the behavior or more sophisticated robots — and also the rats’ one. Read more…

Robots that act like rat pups can tell us something about the behavior of both, according to UC Davis researchers.

Sanjay Joshi, assistant professor of mechanical and aeronautical engineering, and associate professor of psychology Jeffrey Schank have recorded the behavior of rat pups and built rat-like robots with the same basic senses and motor skills to see how behavior can emerge from a simple set of rules.

Here are the basic facts.

Seven to 10-day-old rat pups, blind and deaf, do not seem to do a whole lot. Videotaped in a rectangular arena in Schank’s laboratory, they move about until they hit a wall, feel their way along the wall until their nose goes into a corner, then mostly stay put. Because their senses and responses are so limited, pups should be a good starting point for building robots that can do the same thing.

Joshi’s laboratory built foot-long robots with tapered snouts, about the same shape as a rat pup. The robots are ringed by sensors so that they “feel” when they bump into a wall or corner. They are programmed to stay in contact with objects they touch, as rats do.

Here is a picture of one of these rat-like robots. (Credit: University of California, Davis) This image comes from the Robotics, Autonomous Systems, and Controls Laboratory (RASCAL) web page.

And here is what — unexpectedly — happened.

But when the robotic “rats” were put into a rectangular arena like that used for experiments with real rats, the robots showed a new behavior. They scuttled along the walls and repeatedly bumped into one corner, but favored one wall. Instead of stopping in a corner they kept going, circling the arena.

“When we re-analyzed the animal data, we found that the animals were also favoring one wall over another as they bumped around in corners,” Joshi said. “The robots showed us what to look for in animal studies.”

On the above image, you can see the actual travel paths of a robotic rat pup with instantiated rules (left) and of a 10-day old rat pup (right). (Credit: University of California, Davis)

Now, the question is: what can we expect from these similarities between animals and robots’ behaviors?

The [researchers are] also looking at the behavior that emerges when groups of robotic rats interact using different kinds of rules. This should show biologists what the rats may be doing. Understanding the biology of these simple systems might later inform the design of more sophisticated robots, Joshi said.

For more information, you can read the two following papers.

• A Biorobotic Investigation of Norway Rat Pups (Rattus norvegicus) in an Arena, Adaptive Behavior (PDF format, 13 pages, 448 KB)
  
  
• Development of Autonomous Robotics Technology for the Study of Rat Pups (PDF format, 13 pages, 668 KB) (The second image on this page comes from this paper.)
  

Sources: University of California, Davis, via EurekAlert!, February 14, 2005

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• Robotics
  

I’m often impressed by some scientists’ ideas. But today, I’m a little bit worried, as researchers have genetically modified a common plant, the Indian mustard, to absorb more selenium, a toxic heavy metal found in soils polluted by irrigation wastewater. The transgenic plants were four times more efficient at swallowing selenium than natural ones in a contaminated area of California’s Central Valley, according to articles from Nature and Wired News. These field tests are only experiments, but the researchers also want to add genes to other plants to remove different toxic materials from soils, such as mercury. What would happen if such transgenic plants filled with dangerous chemicals start to crossbreed with natural ones? Or if an insect eats these plants before being eaten itself in the natural food chain, leading to some selenium in our food? Read more and tell me what you think…

Let’s start with the good news from the Nature article.

Genetically modified Indian mustard plants have successfully cleaned up excessive selenium in a California field. This is the first field trial for a pollution-busting transgenic plant, and it proves that the technology can work outside the laboratory, say the researchers who carried out the test.

Farmland in certain parts of California is heavily irrigated, and the water dissolves selenium in shale found in the region. As the water evaporates on the surface soil, selenium is concentrated to levels that are toxic to plants. But Indian mustard (Brassica juncea) has a natural resistance to the element, and absorbs it as it takes in water through its roots.

To increase the level of absorption of selenium by the Indian mustard plants, the researchers, led by Norman Terry, a plant biologist at the University of California, Berkeley, added extra genes to the plant. And here are the first field test results.

The researchers created three different strains of the transgenic mustard plants, each producing different enzymes to soak up selenium, and tested them in selenium-contaminated soils alongside wild-type Indian mustard. [And] hey found that the transgenic plants could accumulate up to 4.3 times as much selenium as conventional, wild-type Indian mustard.

The transgenic plants showed up to 80% of the growth expected in uncontaminated soil, whereas the wild-type plants had their growth halved by the selenium. They were harvested after 45 days in the field, but the researchers expect that longer growth periods could remove more selenium, and estimate that the most effective plants removed about 4.4% of the element in the top 25 centimetres of soil.

The process known as phytoremediation, which uses natural plants to remove toxic materials from soil, is not new, and is cheaper than traditional methods, which imply to remove polluted soil some place before burying it elsewhere. But it takes a long time, so adding genes to speed the process is an attractive solution. But what about the long term ecological impact?

The possibility of the transgenic plants crossbreeding with food crops is a worry, admits Clayton Rugh, a plant biologist at Michigan State University in East Lansing. “If you’re going to engineer a plant to take up high quantities of metals, you must ensure it doesn’t get into food crops,” he says. “They would have to be carefully contained with measures above and beyond those for genetically modified food crops,” he says.

Another source mentioned by Wired News also admits there are some dangers.

“We don’t know enough about the unintended effects of genetic engineering,” said Gurian-Sherman, senior scientist with the Center for Food Safety. The toxicity of plants can change, or a modified plant could interbreed with wild plants, he said. “What happens when an insect eats one of these plants, and then something else eats that insect?

On the contrary, Terry doesn’t seem concerned by the consequences of such experiments. Read carefully this quote from Nature.

In a useful spin-off, the Indian mustard plants could eventually be used as feed for cattle with insufficient selenium in their diet, says Terry. The team is now trying to boost the plants’ power even more. “We’d like to see increases in accumulation of 10 to 100 times that possible with wild-type plants,” says Terry. “This research is a great start.”

Let me summarize this. First, you add genes to a plant which will then easily absorb dangerous and toxic chemicals. Then you use these plants to feed cows. But why on earth a cow would need to ingest more selenium? And are you sure that you want this selenium in your plate?

I’m not an expert in this field, but these experiments look quite dangerous to me in the long term, especially if they become widespread.

By the way, the research work has been published by Environmental Science & Technology on February 1, 2005. Here is a link to the abstract of the paper called “Field Trial of Transgenic Indian Mustard Plants Shows Enhanced Phytoremediation of Selenium-Contaminated Sediment.”

Can we benefit from this or not? Please post your comments and tell me what you think.

Sources: Mark Peplow, Nature, February 11, 2005; Stephen Leahy, Wired News, February 12, 2005; and various websites

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• Nature
  

What is responsible for the evolution of forms and shapes of living organisms? Is this our genes or the DNA mechanisms which control where genes are used in the making of the animal’s body? Scientists from the University of Wisconsin-Madison have found the answer by studying the various spots on the wings of a common fruit fly. In this article, they explain that molecular switches control where the pigmentation is deployed. Common genes are controlled to produce an endless array of patterns, decoration and body architecture found in animals. And it is almost certain that these molecular switches are at work in other animals, including humans. What is even more fascinating is how it works. According to the researchers, evolution is a combination of chance and ecological necessity, which selects those things that are going to be kept. It means that animals’ features are just accidents, but accidents that are preserved because they confer some kind of advantage. Read more…

By analyzing the genetic origin of a modest spot on a fruit fly wing, Howard Hughes Medical Institute (HHMI) researchers have discovered a molecular mechanism that explains, in part, how new patterns can evolve. The secret appears to be specific segments of DNA that orchestrate where proteins are used in the construction of an insect’s body.

The researchers chose to study the evolution of the wing spot on the fruit fly because it is a simple trait with a well-understood evolutionary history. While ancient fruit fly species lack the spots, said HHMI investigator Sean B. Carroll, some species that evolved later have developed them under the pressure of sexual selection. The wing spots offer a survival advantage to males, who depend on the decorations to “impress” females to choose them in the mating process.

You’ll find other pictures on this page which also contains a link to a short movie where you can see “the male fruit fly showing off his wing spots in an effort to get the attention of the ladies.” (QuickTime format, 35 seconds, 10.1 MB).

The research work has been published by Nature on February 3, 2005 under the name “Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila” (Vol. 433, No. 7025, Pages 481 - 487). Here is a link to the abstract.

The gain, loss or modification of morphological traits is generally associated with changes in gene regulation during development. However, the molecular bases underlying these evolutionary changes have remained elusive. Here we identify one of the molecular mechanisms that contributes to the evolutionary gain of a male-specific wing pigmentation spot in Drosophila biarmipes, a species closely related to Drosophila melanogaster. We show that the evolution of this spot involved modifications of an ancestral cis-regulatory element of the yellow pigmentation gene. This element has gained multiple binding sites for transcription factors that are deeply conserved components of the regulatory landscape controlling wing development, including the selector protein Engrailed. The evolutionary stability of components of regulatory landscapes, which can be co-opted by chance mutations in cis-regulatory elements, might explain the repeated evolution of similar morphological patterns, such as wing pigmentation patterns in flies.

Here are few more resources if you’re interested by this findings.

• Sean Carroll’s lab
  
  
• Scientists find portal to how animals evolve
  An article from the University of Wisconsin-Madison
  
  
• A news release from the University of Wisconsin-Madison
  

Sources: Howard Hughes Medical Institute, February 4, 2005, and various websites

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• DNA
  
  
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Scientists from the Wildlife Conservation Society (WCS) are now counting the animals in their Bronx zoo with the help of a satellite orbiting 280 miles above the Earth — and New York. In this news release, they say they’re so pleased with the results that they plan to count wildlife populations in remote locations in other parts of the world. In the months to come, they’ll count “elephants and giraffes in Tanzania, flamingos in South America, and elk, bison and antelope in Wyoming.” They add that you need a “trained eye” to spot the animals, and believe me, it’s true. They released images which look like a bunch of messy pixels to my “untrained eyes.” But read more…

The keyword in the legend above is “trained eye.” Personally, I don’t really spot a giraffe in this satellite image. And you, can you find the giraffe in this larger image?

Here is the introduction of the WCS news release.

Scientists with the Bronx Zoo-based Wildlife Conservation Society (WCS) have recently been counting their zoo animals from a lofty perch: namely, outer space. Using high-tech cameras fixed to an orbiting satellite 280 miles overhead, a WCS scientific team tallied some of the zoo’s own animal collection to see if satellites can help count wildlife populations in remote locations throughout the world.

The WCS team is currently analyzing high-tech maps produced by the satellite, which orbited the zoo last Wednesday, Nov. 10th. So far, everything from giraffes to Thomson’s gazelles have been spotted with startling clarity. If the technology proves accurate, WCS is hopeful that it can be used to monitor endangered wildlife populations that live in hard-to-reach locations.

You’ll find other details in this NASA news release, a slightly rephrased version of the WCS one, but which contains pictures, such as the one above.

Using cameras fixed to an orbiting satellite 450 kilometers (280 miles) overhead, WCS scientists say that they will be able to take high resolution photographs of specific areas to determine the wildlife composition within that area. They will then compare images from different dates to see changes, either population growth or decline, over time. The satellite, called Quickbird, is owned by DigitalGlobe, a private company.

Launched in 2001, QuickBird is still one of the only commercial remote sensing satellites capable of gathering sub-meter resolution. Its subsystem captures 0.61-meter-resolution panchromatic imagery, and 2.4-meter multi-spectral imagery. It will produce 11 x 11-km snapshots to 11 x 225-km strip maps. [These details come from this page at Kodak website.]

For more information about this satellite, you can check the QuickBird Specifications and some QuickBird Satellite Images.

Sources: Wildlife Conservation Society news release, via EurekAlert!, November 17, 2004; NASA news release, January 17, 2005; and various websites

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