2012 October 31 Wednesday
1092 Genomes Sequenced To Show Tens Of Millions Of Variants

We differ from each other genetically in least 40 million ways.

By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38|[thinsp]|million single nucleotide polymorphisms, 1.4|[thinsp]|million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection.

That's really the tip of the iceberg. A study published in May 2012 found one genetic variant in every 17 genetic letters.

The scientists discovered one genetic variant every 17 bases, which was a dramatically higher rate than they expected, said Novembre, a population geneticist who is a member of UCLA's interdepartmental program in bioinformatics.

Most of the time, only one person has the genetic variant and the other 14,001 do not.

To put that in perspective, we've got 2.9 billion bases. That suggests perhaps 170 million genetic variants, most waiting to be found. This makes identifying which ones are functionally significant much harder. It also makes humans more genetically different from each other than we heard when the first human genome was sequenced back in the 1990s.

Since genome sequencing costs are still dropping we are going to see the number of genomes fully sequenced go up by orders of magnitude into the tens of millions and beyond. While the impact of rarer genetic variants will be harder to figure out we will see a huge flood of discoveries on the meaning of more common genetic variants.

We are not many years away from the point where pre-implantation genetic testing of embryos starts to make sense. Once the functional purposes of enough genetic variants become known I expect millions will choose among several embryos to get the best choice of genetic variants for their offspring. Human evolution will start to accelerate at that point.

By Randall Parker 2012 October 31 09:54 PM 
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2012 October 28 Sunday
Companies Plan Natural Gas To Diesel Plant

Oxford Catalysts and Chesapeake Energy Corporation are betting on a long term high ratio of oil to natural gas prices by planning to build natural gas-to-liquid plants.

Oxford Catalysts can produce a barrel of premium diesel for $66, or $1.57 a gallon, using gas at $4 per thousand standard cubic feet ($3.89 per mmBtu) at plants with a capacity of just 1,500 barrels a day. The unprofitable technology developer said a plant that size can be built for about $150 million and would last for 20 years.

The article also surveys efforts by other firms to convert natural gas to liquids (GTL). Some firms are focusing on ways to do GTL on site at small natural gas fields. This would make more natural gas fields economically viable since natural gas transportation from small fields often costs too mujch.

Historically, the cost of a million BTU (mmBTU) of energy from oil has always been higher than the same mmBTU from natural gas because oil, due to its liquid form, is much more useful, especially in transportation. The price ratio has been close to 2. However, due to technological advances in shale natural gas extraction in the United States starting in 2009 the ratio of of the cost of a mmBTU of oil to a mmBTU of natural gas exploded to around 10. If investors become convinced high price ratios will be sustained for a long period then it makes economic sense to build expensive plants to convert natural gas into liquids that can be used in transportation. However, those plants can not pay back their costs if the high price ratio between oil and natural gas turns out to be relatively short lived.

Conversion of cheap US and Canadian natural gas to diesel and other liquid fuels competes with cooling natural gas into liquified natural gas (LNG) for export on big refrigerated LNG ships. Given that Asian natural gas prices are over 5 times higher than American natural gas prices we can expect more natural gas exports as well.

By Randall Parker 2012 October 28 10:20 AM 
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Invasive Species Wipe Out Guam Birds: Therefore More Spiders

The invasive brown treesnake wiped out native birds on Guam. The resulting surge in insect populations created great conditions for spiders to build webs and eat plentiful insects.

In one of the first studies to examine how the loss of forest birds is effecting Guam's island ecosystem, biologists from Rice University, the University of Washington and the University of Guam found that the Pacific island's jungles have as many as 40 times more spiders than are found on nearby islands like Saipan.

The brown treesnake is very hard to find. So it has not been possible to reverse its effects on the bird population of Guam by eradication. What I wonder: Why not build elevated bird nests on poles so that treesnakes can't reach them?

Trying to keep treesnakes out of entire forests costs too much. So why not create really small nesting structures designed to appeal to native Guam birds so they'll nest in safe places? These structures could even have bird food placed on them to attract birds.

Historically, if ecologists wanted to study how insects reacted to the absence of birds, they would build an "exclosure," a covering designed to keep birds out of their study area. Rogers said most exclosures cover a few branches of one tree, and, in rare cases, an entire tree. Building structures large enough to exclude birds from an entire forest simply isn't affordable, so the brown treesnake has effectively set the stage for experiments that ecologists couldn't otherwise do.

Maui has a similar problem with feral cats and rats wiping out native birds. Also, mongooses are a problem. Very thin slippery poles that hold up a flat large tray of dirt could provide a place for vegetation and possibly attract birds to nest on it. If a surface could be designed that looks more attractive to birds than the ground around it perhaps they could be induced to nest where it is safe. Ditto for birds nests in trees. Put artificial bird nests up on very high poles near trees.

Guam has lost many native species as a result of invasive species.

Of 18 species of native Guamanian birds, seven are extinct, two are extinct in the wild (the Guam Rail, pictured left, and the Micronesian Kingfisher survive only in captivity), six are rare, and three are uncommon. Birds were not the only Guamanian animals to suffer; small mammal and reptile faunas have also been reduced in numbers. Five native lizard species have become extinct locally. In some local surveys of small mammals, the only species that were found were the introduced house mouse and the black rat. Shrews have virtually disappeared.

Once it becomes easy to genetically engineer new species the invasive species problem is going to become a whole new ballgame. I think we may witness a huge acceleration in the rate of evolution of not just humans but also many other species as well. Just as we have computer virus and worm hackers today we will have secret gene hackers who create invasive species in order to win fame for the spread of their organisms. They'll probably code a pseudonym into several places in the DNA as their signature that they created each of several organisms that are their claim to fame.

Creation of new species will be easy to do by using future microfluidic devices and computer programs to splice together DNA from different species to create new hybrids. This will be easier for some species than for others. Someone in a rural area could raise birds and could fertilize eggs with pieces of DNA from their microfluidic devices. Then once the baby birds start to grow open up the cages and let them fly away. The ability to capture wild female birds and inject genetically engineered early stage eggs into their ovary apparatus could even allow a genetic engineer to not have to take care of the birds as they sit on their genetically engineered eggs.

By Randall Parker 2012 October 28 08:52 AM 
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Female Closeness Feelings As A Function Of Fertility, Attraction

The truth about human nature is not pretty. Says the headline: "Women with stable but not-so-sexy mates become more distant, critical during periods of high fertility"

Long after women have chosen Mr. Stable over Mr. Sexy, they struggle unconsciously with the decision, according to a new study by UCLA researchers who look at subtle changes in behavior during ovulation.

At their most fertile period, these women are less likely to feel close to their mates and more likely to find fault with them than women mated to more sexually desirable men, the research shows.

"A woman evaluates her relationship differently at different times in her cycle, and her evaluation seems to be colored by how sexually attractive she perceives her partner to be," said Martie Haselton, a professor of psychology and communication studies at UCLA and senior author of the study.

Nevertheless, the negative feelings appear fleeting, and they don't seem to affect a woman's long-term commitment to her romantic relationship, the study found.

"Even when these women are feeling less positive about their relationship, they don't want to end it," said Christina Larson, the study's lead author and a doctoral candidate in social psychology at UCLA.

I'm skeptical of the claim that women less physically attracted to their man are no more likely to leave him.

If men could get results of a closeness survey on their prospective bride before marriage they could find out whether she is going to get closer or further way when she's most fertile. Might be better to avoid marriage if she's not that turned on by you.

Then at two different points in her monthly cycle — at high fertility (just before ovulation) and at low fertility — each woman was asked about the quality of her romantic relationship. The researchers, who used a questionnaire designed exclusively for the study, found no significant change across the cycle in how the women perceived their level of commitment to the relationship or, at least initially, in their satisfaction with it.

But an exercise that required the women to rate how close they felt to their men yielded dramatic results. As women mated to less sexually attractive men moved from their least fertile to most fertile period, their closeness scores dropped one point on a seven-point scale. Women mated to the most sexually attractive men, meanwhile, experienced the opposite effect. As these women moved from their least to most fertile period, their closeness scores rose by a point.

"Women with the really good, stable guy felt more distant at high-fertility periods than low-fertility periods," Haselton said. "That isn't the case with women who were mated to particularly sexually attractive men. The closeness of their relationships got a boost just prior to ovulation."

How to surreptitiously measure this effect?

By Randall Parker 2012 October 28 08:52 AM 
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2012 October 22 Monday
Protein In Aged Muscles Cuts Stem Cell Population

The microenvironment around stem cells in aged tissue may serve as a major obstacle in the way of development or rejuvenation therapies. For example, old blood has a chemical composition that suppresses muscle stem cell replication and repair of old muscle tissue. Old senescent cells accelerate aging by their presence and senescent cells might create a microenvironment for other cells that suppresses their repair work. Now another research team finds evidence that old tissue contains more of a developmental protein that cause a reduction in stem cell supply.

Andrew Brack, PhD, of the MGH Center for Regenerative Medicine, senior and corresponding author of the Nature paper, says, "Just as it is important for athletes to build recovery time into their training schedules, stem cells also need time to recuperate, but we found that aged stem cells recuperate less often. We were surprised to find that the events prior to muscle regeneration had a major influence on regenerative potential. That makes sense to us as humans, in terms of the need to sleep and to eat a healthy diet, but that the need to rest also plays out at the level of stem cells is quite remarkable." An assistant professor of Medicine at Harvard Medical School, Brack is also a principal faculty member at the Harvard Stem Cell Institute.

Once we have the ability to create high quality stem cells of each type used by the body will they work when injected into various tissue types? Or will the proteins and other chemical compounds getting excreted from aging tissue suppress the stem cells and prevent them from doing repairs on the damage that accumulates in aging tissue? The protein FGF2 might be one of the obstacles on the road to aged tissue regeneration.

In a series of experiments in mice, the authors found that a developmental protein called fibroblast growth factor-2 (FGF2) is elevated in the aging muscle stem cell microenvironment and drives stem cells out of the dormant state. Satellite cells that are forced to replicate lose the ability to maintain their identity as stem cells, reducing the stem cell population."

Block FGF2 and get more muscle tissue repair.

The authors also found that blocking the age-related increase in FGF signaling both in aged satellite cells or in the cellular microenvironment protected against stem cell loss, maintained stem cell renewal during aging and dramatically improved the ability of aged muscle tissue to repair itself.

It might not be prudent to turn on old stem cells to divide more. The benefits of tissue repair have to be weighed against heightened risk of cancer that would come with turning up the rate at which stem cells divide. Though once we have great cures for cancer with minimal side effects the benefits of turning up replication in aged stem cells would probably outweigh the risks.

It may not be enough to just deliver youthful stem cells into aged tissue. We might also need the ability to manipulate the chemicals in the tissue environment so that stem cells will be free to do repair.

Lead author Joe Chakkalakal, PhD, a research fellow in Brack's lab, says, "This work highlights the usefulness of targeting the aged stem cell or its environment to protect stem cells and the tissues they serve from the effects of aging."

By Randall Parker 2012 October 22 09:45 PM  Rejuvenation Tissue
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2012 October 16 Tuesday
Stem Cells Restore Thyroid Function In Mice

A paper in Nature reports successful regeneration of thyroid function in mice using embryonic stem cells. Another step in the direction of body repair by replacing body parts.

Sabine Costagliola, a molecular embryologist at the Free University of Brussels, and her team study the development of the thyroid gland, which regulates how the body uses energy and affects sensitivity to other hormones. Their research shows that thyroid function can be re-established even after the gland has been destroyed — at least in mice.

Once this ability to grow replacement organs is replicated in humans we'll start being able to repair our bodies the same way repair our cars: by replacing bad parts.

Body part replacement has uses beyond restoring youthful function. If we could replace, say, a pancreas than has cancer in it then getting rid of cancer by swapping ot cancerous organs would become the preferred treatment in many cases.

By Randall Parker 2012 October 16 09:43 PM 
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Earth Sized Planet 4.4 Light Years Away

In the Alpha Centauri triple star system an Earth-sized planet orbits Alpha Centauri B but too close for comfort.

It is presumably a rocky ball like our own, but it is not habitable. It circles Alpha Centauri B, a reddish orb about half as luminous as the Sun, every three days at a distance of only about four million miles, resulting in hellish surface temperatures of 1,200 degrees.

Imagine we could move that planet into a higher (and cooler) orbit. Well, since it is so hot now it probably has little hydrogen left. So terraforming seems problematic unless the Alpha Centauri system also has a frozen planet in a much higher orbit that could supply the needed water. The energy costs of moving a planet to a higher orbit and also moving hydrogen and oxygen off a frozen planet and into a lower orbit seem prohibitive But maybe 100 years from now the challenge might seem much easier.

By Randall Parker 2012 October 16 09:15 PM 
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2012 October 14 Sunday
Computers Gradually Taking Over More Driving Decisions

Collision avoidance systems are already available as an option on some cars. If you can afford such systems then get them on your next car. Remember my motto: first, don't die.

The second highest cause of automobile crashes is rear-end collisions – 17 percent. Thousands of people die. The solution? "It is simple," said Clay Gabler, a professor of biomedical engineering at Virginia Tech. "Slow the striking vehicle."

The concept is simple. Execution is complex and expensive. But in a life-and-death scenario, it is worth the investment, agree Gabler and Kristofer Kusano of Herndon, Va., a doctoral student in mechanical engineering. In affiliation with the Virginia Tech-Wake Forest Center for Injury Biomechanics and the Virginia Tech Transportation Institute, they are conducting research on the potential benefit of a suite of collision avoidance systems now available as options on some new cars.

We aren't jumping directly from the human-operated car to the computer-operated car. Rather, a progression of successively more powerful computers are gradually taking over more driving decisions, especially in more dangerous situations. One of the first such, anti-lock braking systems (or ABS), really enhanced the performance of the car to carry out the driver's intent. Ditto with Electronic Stability Control (ESC). But automated collision avoidance systems take an important step beyond ABS or ESC by deciding on their own to attempt to avoid a collision. So this is a Rubicon of sorts. We are going to start letting computers to initiate some driving decisions.

Not surprisingly, computers can do a faster and better job at deciding to take steps to avoid a collision. How about slashing serious injuries and deaths by 50%?

Their research, which has been published in peer-reviewed journals, predicts that the use of three systems may reduce serious injuries by 50 percent.

Gabler and Kusano are looking at three systems that can operate independently or in sequence to prevent or mitigate a front collision. They have looked at one generic system that begins with a warning 1.7 seconds before a potential crash. Once alerted, if the driver begins to apply the brakes, there is brake assistance. "The car says, 'Let me show you how to do it more effectively and applies the necessary braking force'," said Gabler.

Finally, 0.45 seconds before the collision, the car will add 0.6 G to the braking effort, or if there is no braking, will apply the brakes autonomously.

20 years from now it would not surprise me if car accident deaths are 90+% lower than they are now and humans make few driving decisions. It'll be the old cars that are responsible for most road deaths and the cry will be heard to either force those cars off the road or upgrade their electronics to put them under computer control.

By Randall Parker 2012 October 14 11:28 AM  Robotics Cars
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Star Trek Tricorder Too Big

The first device that is like the Star Trek tricorder medical monitoring device (as used by Dr. McCoy) will probably be much smaller than a tricorder.

UNIVERSITY PARK, Pa. -- A technique that uses acoustic waves to sort cells on a chip may create miniature medical analytic devices that could make Star Trek's tricorder seem a bit bulky in comparison, according to a team of researchers.

Think about McCoy or Spock staring into some scientific instrument on a bench. In all likelihood humans won't stare at cells under a microscope when instead microfluidic devices with lots of built-in sensors will do all the data collection.

The device uses two beams of acoustic -- or sound -- waves to act as acoustic tweezers and sort a continuous flow of cells on a dime-sized chip, said Tony Jun Huang, associate professor of engineering science and mechanics, Penn State. By changing the frequency of the acoustic waves, researchers can easily alter the paths of the cells.

Huang said that since the device can sort cells into five or more channels, it will allow more cell types to be analyzed simultaneously, which paves the way for smaller, more efficient and less expensive analytic devices.

"Eventually, you could do analysis on a device about the size of a cell phone," said Huang. "It's very doable and we're making in-roads to that right now."

An increasing portion of all medical testing won't be done in labs. It will be done by a handheld device that either the doctor or patient uses. The device will upload collected data wirelessly to a web server that will run medical diagnostic logic and offer treatment recommendations. We will have all this long before humans colonize Mars, let alone travel between the stars.

Miniaturization is the key enabling trend in technology. Without miniaturization of factories, lab tests, and computing migration of humans to other planets would be too hard.

Update: Cell phones and web servers will monitor for changes in your habits to detect mental and physical health problems. Add some sensors embedded into your body (or even worn like a watch or pendant) that the cell phones can interrogate and then the constant monitoring will be able to detect many more problems and much more quickly. Some of those sensors embedded in your body will dissolve after collecting needed data.

By Randall Parker 2012 October 14 10:04 AM  Biotech Assay Tools
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2012 October 07 Sunday
Restraint On Global Fishing Could Boost Future Yields

Better policies could help boost fishery productivity.

A study published in Science magazine contains new population assessments for thousands of fisheries around the globe, providing insight on the health of data-poor fisheries that account for more than 80 percent of the world's catch. The research confirms suspicions that these fisheries are in decline, but it also highlights hope for the future: most of these fisheries have not yet collapsed. If we act quickly to prevent overfishing and allow depleted stocks to recover to sustainable levels, they could provide more seafood over the long-term. This could increase the amount of fish brought to shore by 8-40 percent on average - and more than double it in some areas - compared to yields predicted if we continue current fishing trends.

But on a global scale the odds of better policies seem slim to me. The political map of Africa especially seems to work against good policies. Too many different countries have borders on the ocean. Fish that don't get fished for off of one country will get fished for in the next country. That contrasts with the United States, Canada, and Russia which have very long ocean borders. Coordination of restraints on fishing are far easier to achieve if the country that refrains from overfishing in its own waters will reap most of benefits.

Even if the yields could be increased the potential increase is a fixed max which is not huge. Most people aren't going to be able eat wild fish. The future of fish production growth has got to be from farmed fish. The wilds can't produce enough to feed the world. The human population has become too large for that.

By Randall Parker 2012 October 07 09:36 PM  Environment Fisheries
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Blood Test Catches Breast And Lung Cancer Earlier

If cancer can be detected before metastasis and completely removed by surgery then effectively it can be cured. Also, the earlier stage detection allows treatments a higher chance of success because at earlier stage the cancers have developed fewer defensive mutations against chemo agents. Well, a couple of Kansas State researchers have developed a blood test that works before clinical symptoms for two major cancers with a test for pancreatic cancer coming soon.

In less than an hour, the test can detect breast cancer and non-small cell lung cancer -- the most common type of lung cancer -- before symptoms like coughing and weight loss start. The researchers anticipate testing for the early stages of pancreatic cancer shortly.

The test was developed by Stefan Bossmann, professor of chemistry, and Deryl Troyer, professor of anatomy and physiology. Both are also researchers affiliated with Kansas State University's Johnson Cancer Research Center and the University of Kansas Cancer Center. Gary Gadbury, professor of statistics at Kansas State University, helped analyze the data from tests with lung and breast cancer patients. The results, data and analysis were recently submitted to the Kansas Bio Authority for accelerated testing.

When early stage blood tests for cancer detection become available it would help if we did not have to go to a doctor's office during normal business hours to get these tests done. One should be able to go to a pharmacy after work, or even at quarterly sessions at bigger businesses, to give blood for early stage disease detection tests. When tests become much more powerful and beneficial they should become far easier to get done.

Imagine detection of cancer at stage 0.

A blood sample from each participant was tested three times. Analysis of the data showed a 95 percent success rate in detecting cancer in participants, including those with breast cancer in stages 0 and 1 and those with lung cancer in stages 1 and 2.

Really early stage detection will bring with it the problem of finding the cancer. The smaller it is the harder it'll be to locate.

By Randall Parker 2012 October 07 09:26 PM  Biotech Cancer
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Robotic Surgery Faster And Better For Neck Tumors

Better living thru robotics.

COLUMBUS, Ohio – Robotic surgery though the mouth is a safe and effective way to remove tumors of the throat and voice box, according to a study by head and neck cancer surgeons at the Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James).

This is the first report in the world literature illustrating the safety and efficacy of transoral robotic surgery for supraglottic laryngectomy, the researchers say.

We need robotic surgery to cut costs and reduce accidents. We especially need robotic surgery to swap out old organs for new organs once organ growth in vats becomes practical. Replacement organs created by tissue engineering are going to be a key rejuvenation therapy. Only robots will be fast enough and safe enough to do organ swapping on the scale that will be required for full body rejuvenation.

If you get cancer in your supraglottic region a robot can handle it better.

The preliminary study examined the outcomes of 13 head and neck cancer patients with tumors located in the region of the throat between the base of the tongue and just above the vocal cords, an area known as the supraglottic region.

Less blood loss, one eighth the amount of surgical time, and a far faster recovery.

The study found that the use of robot-assisted surgery to remove these tumors through the mouth took about 25 minutes on average, and that blood loss was minimal – a little more than three teaspoons, or 15.4 milliliters, on average, per patient. No surgical complications were encountered and 11 of the 13 patients could accept an oral diet within 24 hours.

If, on the other hand, these tumors are removed by performing open surgery on the neck, the operation can take around 4 hours to perform, require 7 to 10 days of hospitalization on average and require a tracheostomy tube and a stomach tube, the researchers say.

Since medical costs are now about 18% of the US economy (and growing) automation of medicine can go far to raise living standards. Plus, we need medical automation in order to deliver rejuvenation therapies on the scale required for full body rejuvenation. Robotics for a longer life in a more youthful body!

By Randall Parker 2012 October 07 04:18 PM  Robots Medicine
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2012 October 06 Saturday
Computer Algorithms To Replace Art Critics?

Categorization of great art can be done by special computer software

Southfield, MI - - Understanding and evaluating art has widely been considered as a task meant for humans, until now. Computer scientists Lior Shamir and Jane Tarakhovsky of Lawrence Technological University in Michigan tackled the question "can machines understand art?" The results were very surprising. In fact, an algorithm has been developed that demonstrates computers are able to "understand" art in a fashion very similar to how art historians perform their analysis, mimicking the perception of expert art critiques.

Was this fully an exercise in software development to create the classification algorithms? Or was a machine learning system doing most of the work? Imagine a literary critic machine learning system that can tell you which books you'll like. It would be much harder to game than Amazon reader reviews. One could get trusted reviews of books. Plus. authors could test their books against the machine learning system to find out whether they've written something with sufficient appeal.

High Renaissance, Baroque, and other categories were identified by the computer program.

In the experiment, published in the recent issue of ACM Journal on Computing and Cultural Heritage, the researchers used approximately 1,000 paintings of 34 well-known artists, and let the computer algorithm analyze the similarity between them based solely on the visual content of the paintings, and without any human guidance. Surprisingly, the computer provided a network of similarities between painters that is largely in agreement with the perception of art historians.

The analysis showed that the computer was clearly able to identify the differences between classical realism and modern artistic styles, and automatically separated the painters into two groups, 18 classical painters and 16 modern painters. Inside these two broad groups the computer identified sub-groups of painters that were part of the same artistic movements. For instance, the computer automatically placed the High Renaissance artists Raphael, Leonardo Da Vinci, and Michelangelo very close to each other. The Baroque painters Vermeer, Rubens and Rembrandt were also clustered together by the algorithm, showing that the computer automatically identified that these painters share similar artistic styles.

Steve Pearlstein argues for continued low productivity growth in service industries. But my expectation is that computer software will become powerful enough to replace many kinds of professional workers.

No matter how innovative people were in coming up with new technology and new ways of organizing their work, Baumol and Bowen reasoned, it would still take a pianist the same 23 minutes to play a Mozart sonata, a barber 20 minutes to cut the hair of the average customer and a first-grade teacher 12 minutes to read her class “Green Eggs and Ham.” Based on this observation, the duo predicted that the cost of education and health care would inevitably outstrip the price of almost everything else.

The kids could interact with an AI that shows up in a hologram. A robotic hair cutting system could cut your hair with 10 pairs of scissors in a few minutes. Well, you might watch a human play a piano. But if you do not need to watch why not have a computer play it?

By Randall Parker 2012 October 06 10:33 PM  AI Service Provision
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