Study sheds light on what causes cells to divide

When a rapidly-growing cell divides into two smaller cells, what triggers the split? Is it the size the growing cell eventually reaches? Or is the real trigger the time period over which the cell keeps growing ever larger?

A novel study published online in the journal Current Biology has finally provided an answer to this long unsolved conundrum. And it's not what many biologists expected.

"How cells control their size and maintain stable size distributions is one of the most fundamental, unsolved problems in biology," said Suckjoon Jun, an assistant professor of physics and molecular biology at UC San Diego, who headed the research study with Massimo Vergassola, a professor of physics. "Even for the bacterium E. coli, arguably the most extensively studied organism to date, no one has been able to answer this question."

Finding a solution was more than a basic-science pursuit for the scientists, who pointed out that learning more about the triggers of cell division would enable researchers to better understand such processes as the runaway cell division that leads to cancer. To conduct the study, Jun and his colleagues developed a tiny device to isolate and physically manipulate individual genetic materials.

"It turned out that we can use this device to also follow the life history of thousands of individual bacterial cells for hundreds of generations," he said. "We looked at the growth patterns of the cells very, very carefully, and realized that there is something really special about the way the cells control their size."

"In our study, we monitored the growth and division of hundreds of thousands of two kinds of bacterial cells, E. coli and B. subtilis, under a wide range of tightly controlled steady-state growth conditions," said Jun. "This produced statistical samples about three orders of magnitude, or a thousand times better, than those previously available. We could thus pursue an unprecedented level of quantitative analysis."

The scientists found through their development of mathematical models that matched their experimental data that the growth of cells followed the growth law, essentially exponential growth based on a constant rate. But they also found to their surprise that cell size or the time between cell divisions had little to do with when the cells divided. Instead, to keep the distribution of different sized cells within a population constant, the cells followed what the researchers termed "an extraordinarily simple quantitative principle of cell-size control."

"Specifically, we showed that cells sense neither space nor time, but add constant size irrespective of their birth size," said Jun. "This 'adder' principle automatically ensures stability of size distributions."

"E. coli and B. subtilis are one billion years divergent in evolution, and they are the textbook examples of the diversity of molecular details for biological controls in different bacterial species. Thus, their sharing the same quantitative principle for size maintenance is a textbook level discovery."

Story Source:

The above story is based on materials provided by University of California - San Diego . The original article was written by Kim McDonald. Note: Materials may be edited for content and length.

Microsoft May Soon Replace Internet Explorer With a New Web Browser

Jim Merithew/WIRED

Microsoft’s Windows 10 operating system will debut with an entirely new web browser code-named Spartan, according to a report citing anonymous sources.

ZDNet’s Mary Jo Foley reports that this new browser is a departure from Internet Explorer, the Microsoft browser whose relevance has waned in recent years. According to Foley, it will be a “lightweight” browser that looks and feels more like the Google Chrome and Mozilla Firefox browsers. But her sources also indicate that Spartan will be offered alongside IE when Windows 10 debuts next year.

With Mozilla Firefox and Google Chrome grabbing so much of the desktop market—and Apple Safari, Google Chrome, and Google’s Android browser dominating the mobile market—Internet Explorer is no longer the force it once was. There was a time when it handled about over 90 percent of all web traffic on desktop and laptop machines, but according to research outfit Net Applications, its share has now dropped to 58 percent. On mobile, its share is about 2 percent.

Spartan attempts to address both these markets, according to Foley. Windows 10 is designed to run across a wide range of devices, and according to Foley, the new browser will be available on phones and tablets as well as laptops and desktops. It’s unclear whether Spartan will run on Android, Apple’s iOS, and other operating systems that compete with Windows, but Foley says there’s a chance it will.

Under new CEO Satya Nadella, the company realizes that, in the modern world, its software must run on more than just Windows. In March, Microsoft revealed a new version of Microsoft Office for the Apple iPad. In November, it debuted free versions of Word, Excel, and Powerpoint versions for the iPhone. And earlier this month, the company acquired the mobile email startup Acompli, an email client compatible on both iOS and Android mobile operating systems.

Microsoft May Replace Internet Explorer With New Web Browser

Jim Merithew/WIRED

Microsoft’s Windows 10 operating system will debut with an entirely new web browser codenamed Spartan, according to a report citing anonymous sources.

ZDNet’s Mary Jo Foley reports that this new browser is a departure from Internet Explorer, the Microsoft browser whose relevance has waned in recent years. According to Foley, it will be a “lightweight” browser that looks and feels more like the Google Chrome and Mozilla Firefox browsers. But her sources also indicate that Spartan will be offered alongside IE when Windows 10 debuts next year.

With Mozilla Firefox and Google Chrome grabbing so much of the desktop market—and Apple Safari, Google Chrome, and Google’s Android browser dominating the mobile market—Internet Explorer is no longer the force it once was. There was a time when it handled about over 90 percent of all web traffic on desktop and laptop machines, but according to research outfit Net Applications, its share has now dropped to 58 percent. On mobile, its share is about 2 percent.

Spartan attempts to address both these markets, according to Foley. Windows 10 is designed to run across a wide range of devices, and according to Foley, the new browser will be available on phones and tablets as well as laptops and desktops. It’s unclear whether Spartan will run on Android, Apple’s iOS, and other operating systems that compete with Windows, but Foley says there’s a chance it will.

Under new CEO Satya Nadella, the company realizes that, in the modern world, its software must run on more than just Windows. In March, Microsoft revealed a new version of Microsoft Office for the Apple iPad. In November, it debuted free versions of Word, Excel, and Powerpoint versions for the iPhone. And earlier this month, the company acquired the mobile email startup Acompli, an email client compatible on both iOS and Android mobile operating systems.

When Enterprises Become Carriers

globochem/Flickr

Communication is a critical function for any business. Listening to customers. Negotiating with suppliers. Collaborating with teams and partners. Without it, no business can thrive or survive. In the past, businesses of all sizes were dependent on carriers for all of these services. According to Standard & Poor’s 2013 Global Sales Report, 46 percent of the S&P 500 business occurs outside of the United States, which is up from 42 percent ten years earlier. Accordingly, telecommunications requirements are more global than ever before.

Connecting these international and disparate company footholds has required a complicated and often expensive combination of voice and data carrier expertise. But the long promised convergence of voice and data networks has enabled savings as IT and Telecom requirements and functions merged into an increasingly common set of products, services and skills. Today, the end of the PSTN and obsolescence of the Hardware PBX is clearly on the horizon, and it’s a reality that must be addressed.

People in their work lives, much like in their consumer ways, have gravitated toward a cloud and mobile-first strategy. Unified communications (UC) software and cloud communications have effectively represented a fork in the road for business communications, with smaller organizations outsourcing and larger enterprises insourcing.

Hence, multi-national enterprises today are able to operate more like Telcos. For example, UC software platforms allow them to replace hardware PBX with software that they manage in their own servers or from cloud based resources.

Outsource, Insource or Federate?

Outsource

For smaller organizations, the trend seems to be going in the other direction. Instead of owning their own PBX and email systems and relying on a carrier for the connectivity, their software goes out into the network as well, and is leased on a low operational expenditure monthly basis.

Insource

Larger global multi-national organizations typically choose to own the software and manage it on a Cloud basis. But they no longer have to order local loop services from an incumbent or CLEC country by country; global carriers can help them consolidate into higher volume arrangement. In doing so, they can also choose to further optimize their costs by thinking like carriers themselves. They are able to create their own Least-Cost-Routing tables with multiple SIP trunking termination providers to reduce the cost of long-distance, off-net calling. They can source local telephone numbers in dozens of countries for contact center, conferencing and office phones via Global SIP DID providers.

UC Platforms like Microsoft Lync and others have put the tools into enterprise hands with the promise of fully integrated systems for email, messaging, voice, fax and conferencing via one platform, but enabled by wholesale priced origination and termination partners for voice, fax, and SMS.

The business case and technical feasibility for unplugging local PRIs and replacing them with globally aggregated data networks, coupled with inbound DIDs and outbound calling, is one that many multi-national corporations are now exploring. Instead of procuring local PRIs, the corporate can order telephone numbers via a Cloud provider and map them to the devices as needed. They can then aggregate their global numbers and outbound termination and secure better wholesale pricing, just like the carriers themselves do.

On an engineering level, the organization will be able to centrally manage and control telecom as inbound calls arrive via SIP, rather than from all over the world via local loop into a regional office. Inbound calls to the telephone number are forwarded via IP enabled carrier networks to Session Border Controllers, and then on to UC systems, call center ACDs or conference bridges for further routing within the organization. Calls can be rerouted as needed; if an employee relocates they need only plug in their SIP phone to reconnect and get back to work. If the business requires a new local number for a new hire, or needs to support a project in a different country, IT can order one and map it instantly to that employees SIP address. The employee could even do it themselves using an API enabled portal.

In this scenario, organizations also benefit from disaster recovery, as global carriers can reroute inbound calls via redundant networks. This saves the IT manager valuable time and frees up personnel and other human resources to focus on bringing the organization back online after a crisis.

Federate

Other trends show that enterprises are also banding together into federations to enable industry-wide communication. Federating voice and video across enterprises, based on a shared and interoperable UC platform vendor, will allow more on-net calling. This can eliminate long-distance charges as well as enable more sophisticated services, such as HD voice codecs and video telephony.

Security Implications

When choosing how to handle their communications – especially if they opt for insourcing – enterprises must consider the security implications. Scandals ranging from hacker-data theft, security holes in carrier communications services to perceived government overreach have created an environment of anxiety about the privacy of telecom. One widely-touted advantage of Microsoft Lync Unified Communication systems that many enterprises find attractive is the encryption of all communication between servers using TLS and SRTP.

Security concerns are particularly acute in the banking and finance segment of enterprise communication, resulting in an increasing premium on self-reliance for carrier services and software. In fact, in October 2014 a consortium of banks – led by Goldman Sachs – announced it had invested in a small Silicon Valley messaging start-up called Perzo, focused on encrypted IP communications, to develop a secure communications platform for their own internal and industry-wide use.

Fork in the Road

Cloud computing, virtualization and UC software have enabled enterprises to benefit from Telco-like economics of scale and efficiencies, and they can now purchase their voice and data services as if they were large carriers. Enterprises are looking at the fork in the road, with one path leading to increased outsourcing, the other to insourcing. Carriers are increasingly focusing on APIs, security, developer outreach and SaaS models to make sure they stay along for the ride for both strategic directions, rather than finding themselves left behind.

Hugh Goldstein is VP of Strategic Alliances at Voxbone.

These Egg-Shaped Speakers Sound So Good, They’ll Scramble Your Brains

Liana Bandziulis

One of the best-sounding small speaker systems we’ve heard this year is also one of the most expensive: The Fujitsu Ten Eclipse TD-M1 Wireless Speaker System, which costs $1,300. Bananas, yes. But queue up Von Karajan’s rendition of the Ninth, kick back in your Dieter Rams 620 chair, give the volume control a liberal nudge, and you’ll be feeling no remorse about the price.

They’re beautiful to behold. Each speaker is 9.5 inches tall and roughly the size of an NFL football, but with gentler curves. At the front of each enclosure is a 3-inch driver that’s covered by a white grill—with the grills on, the enclosures’ egg-shaped profiles are near seamless. Inside are 20-watt digital amps (one per channel) and a DAC for the whole system.

There are two wireless options. One is Apple’s AirPlay, and the other is a Wi-Fi direct mode that enables you to set up a one-to-one connection with a phone or tablet without needing to connect everything to the same network. Wired options include USB digital inputs (for playing your 192kHz/24-bitsources) as well as an analog 3.5-mm mini connection (for your cassette Walkman). But if you just want to run them as wireless speakers, you only have to plug them into power outlets. A free iOS app serves as a remote.

The sound? Lively and sparkling. Place the speakers about ten feet apart, plant yourself in the sweet spot, and they will reproduce live and studio recordings with impressive accuracy. Delicate stuff in particular—acoustic guitar music, vocal jazz—jumps to life. Bass frequencies are meaty and don’t sound the slightest bit artificial. And unlike many small speakers, the Eclipses sound best when you turn them up nice and loud.

Because they plug into AC outlets, these would work best as PC speakers on a desk, or as main speakers in a small listening room. Bookshelf speakers, maybe not so much. But their striking, unconventional design and excellent sound makes them a welcome visual and aural upgrade anywhere you’re currently harboring that pair of boring old black boxes.

When Enterprises Become Carriers

globochem/Flickr

Communication is a critical function for any business. Listening to customers. Negotiating with suppliers. Collaborating with teams and partners. Without it, no business can thrive or survive. In the past, businesses of all sizes were dependent on carriers for all of these services. According to Standard & Poor’s 2013 Global Sales Report, 46 percent of the S&P 500 business occurs outside of the United States, which is up from 42 percent ten years earlier. Accordingly, telecommunications requirements are more global than ever before.

Connecting these international and disparate company footholds has required a complicated and often expensive combination of voice and data carrier expertise. But the long promised convergence of voice and data networks has enabled savings as IT and Telecom requirements and functions merged into an increasingly common set of products, services and skills. Today, the end of the PSTN and obsolescence of the Hardware PBX is clearly on the horizon, and it’s a reality that must be addressed.

People in their work lives, much like in their consumer ways, have gravitated toward a cloud and mobile-first strategy. Unified communications (UC) software and cloud communications have effectively represented a fork in the road for business communications, with smaller organizations outsourcing and larger enterprises insourcing.

Hence, multi-national enterprises today are able to operate more like Telcos. For example, UC software platforms allow them to replace hardware PBX with software that they manage in their own servers or from cloud based resources.

Outsource, Insource or Federate?

Outsource

For smaller organizations, the trend seems to be going in the other direction. Instead of owning their own PBX and email systems and relying on a carrier for the connectivity, their software goes out into the network as well, and is leased on a low operational expenditure monthly basis.

Insource

Larger global multi-national organizations typically choose to own the software and manage it on a Cloud basis. But they no longer have to order local loop services from an incumbent or CLEC country by country; global carriers can help them consolidate into higher volume arrangement. In doing so, they can also choose to further optimize their costs by thinking like carriers themselves. They are able to create their own Least-Cost-Routing tables with multiple SIP trunking termination providers to reduce the cost of long-distance, off-net calling. They can source local telephone numbers in dozens of countries for contact center, conferencing and office phones via Global SIP DID providers.

UC Platforms like Microsoft Lync and others have put the tools into enterprise hands with the promise of fully integrated systems for email, messaging, voice, fax and conferencing via one platform, but enabled by wholesale priced origination and termination partners for voice, fax, and SMS.

The business case and technical feasibility for unplugging local PRIs and replacing them with globally aggregated data networks, coupled with inbound DIDs and outbound calling, is one that many multi-national corporations are now exploring. Instead of procuring local PRIs, the corporate can order telephone numbers via a Cloud provider and map them to the devices as needed. They can then aggregate their global numbers and outbound termination and secure better wholesale pricing, just like the carriers themselves do.

On an engineering level, the organization will be able to centrally manage and control telecom as inbound calls arrive via SIP, rather than from all over the world via local loop into a regional office. Inbound calls to the telephone number are forwarded via IP enabled carrier networks to Session Border Controllers, and then on to UC systems, call center ACDs or conference bridges for further routing within the organization. Calls can be rerouted as needed; if an employee relocates they need only plug in their SIP phone to reconnect and get back to work. If the business requires a new local number for a new hire, or needs to support a project in a different country, IT can order one and map it instantly to that employees SIP address. The employee could even do it themselves using an API enabled portal.

In this scenario, organizations also benefit from disaster recovery, as global carriers can reroute inbound calls via redundant networks. This saves the IT manager valuable time and frees up personnel and other human resources to focus on bringing the organization back online after a crisis.

Federate

Other trends show that enterprises are also banding together into federations to enable industry-wide communication. Federating voice and video across enterprises, based on a shared and interoperable UC platform vendor, will allow more on-net calling. This can eliminate long-distance charges as well as enable more sophisticated services, such as HD voice codecs and video telephony.

Security Implications

When choosing how to handle their communications – especially if they opt for insourcing – enterprises must consider the security implications. Scandals ranging from hacker-data theft, security holes in carrier communications services to perceived government overreach have created an environment of anxiety about the privacy of telecom. One widely-touted advantage of Microsoft Lync Unified Communication systems that many enterprises find attractive is the encryption of all communication between servers using TLS and SRTP.

Security concerns are particularly acute in the banking and finance segment of enterprise communication, resulting in an increasing premium on self-reliance for carrier services and software. In fact, in October 2014 a consortium of banks – led by Goldman Sachs – announced it had invested in a small Silicon Valley messaging start-up called Perzo, focused on encrypted IP communications, to develop a secure communications platform for their own internal and industry-wide use.

Fork in the Road

Cloud computing, virtualization and UC software have enabled enterprises to benefit from Telco-like economics of scale and efficiencies, and they can now purchase their voice and data services as if they were large carriers. Enterprises are looking at the fork in the road, with one path leading to increased outsourcing, the other to insourcing. Carriers are increasingly focusing on APIs, security, developer outreach and SaaS models to make sure they stay along for the ride for both strategic directions, rather than finding themselves left behind.

Hugh Goldstein is VP of Strategic Alliances at Voxbone.

These Egg-Shaped Speakers Sound So Good, They’ll Scramble Your Brains

Liana Bandziulis

One of the best-sounding small speaker systems we’ve heard this year is also one of the most expensive: The Fujitsu Ten Eclipse TD-M1 Wireless Speaker System, which costs $1,300. Bananas, yes. But queue up Von Karajan’s rendition of the Ninth, kick back in your Dieter Rams 620 chair, give the volume control a liberal nudge, and you’ll be feeling no remorse about the price.

They’re beautiful to behold. Each speaker is 9.5 inches tall and roughly the size of an NFL football, but with gentler curves. At the front of each enclosure is a 3-inch driver that’s covered by a white grill—with the grills on, the enclosures’ egg-shaped profiles are near seamless. Inside are 20-watt digital amps (one per channel) and a DAC for the whole system.

There are two wireless options. One is Apple’s AirPlay, and the other is a Wi-Fi direct mode that enables you to set up a one-to-one connection with a phone or tablet without needing to connect everything to the same network. Wired options include USB digital inputs (for playing your 192kHz/24-bitsources) as well as an analog 3.5-mm mini connection (for your cassette Walkman). But if you just want to run them as wireless speakers, you only have to plug them into power outlets. A free iOS app serves as a remote.

The sound? Lively and sparkling. Place the speakers about ten feet apart, plant yourself in the sweet spot, and they will reproduce live and studio recordings with impressive accuracy. Delicate stuff in particular—acoustic guitar music, vocal jazz—jumps to life. Bass frequencies are meaty and don’t sound the slightest bit artificial. And unlike many small speakers, the Eclipses sound best when you turn them up nice and loud.

Because they plug into AC outlets, these would work best as PC speakers on a desk, or as main speakers in a small listening room. Bookshelf speakers, maybe not so much. But their striking, unconventional design and excellent sound makes them a welcome visual and aural upgrade anywhere you’re currently harboring that pair of boring old black boxes.

Etna Has First Intense Eruption in Over a Year

The glowing New Southeast Crater during the eruption of Etna on December 28, 2014. Image taken from video by Alessandro Lo Piccolo / YouTube.

It has been a quiet year for Italy’s Etna, but as if to remind everyone that the volcano is almost always ready to erupt, Etna produced its most intense eruption (“paroxysm” in the lingo of the Osservatorio Etneo) since December 2013. This eruption from the New Southeast Crater had all the classic pieces of an Etna eruption – lava fountains, lava flows and ash fall that covered the region with dark grey volcanic debris. However, as intense as it was, it was also brief, ending within a few hours of starting and by this morning, Etna was merely steaming in the morning sun (see below). You can check out some video of the eruption taken last night by Alessandro Lo Piccolo, where the ash-and-steam column is clearly seen glowing red (see above, likely reflecting the light from the lava fountains and lava flows).

The steaming crater of Etna seen on the morning of December 29, 2014, following the previous night’s paroxysm. Photo by Dr. Boris Behncke, used by permission.

Etna’s eruption is a great reminder that you still have 2 days to vote for the 2014 Pliny for Volcanic Event of the Year. Cast your ballot by December 31 to be counted!

Holiday Physics Homework

Rhett Allain

It’s that time of year. Christmas, New Years, and other holiday stuff. Now you can just sit around in your pajamas and watch football. Or can you? Don’t forget your holiday physics homework.

Before I post your homework, I am going to give you an example. If I don’t give an example, everyone gets angry. So here it is (yes, this is an old problem with new data).

How Fast Is That Nerf Dart?

Everyone loves Nerf guns. Also, if you borrow your wife’s phone you can easily make a slow motion video.

Slow motion video at 240 fps.

This is a 240 fps video from the iPhone 6 (here is a youtube version). It’s a little difficult to see, but there is also a meterstick on the ground for scaling. You should know what comes next – video analysis with Tracker Video Analysis. I’ll just skip all the details (but here is a quick video analysis tutorial) and go straight to a plot of the position of the dart.

Since the dart was shot at an angle, I have included plots for both the x- and y-position. Looking at the slope, this gives an x-velocity of 19.2 m/s and a y-velocity of 3.04 m/s. This gives an average magnitude of 19.44 m/s. This speed is quite a bit faster than this other Nerf gun I tested at around 10 m/s.

See. That’s not so difficult of a homework problem. Actually, you could take this one step farther. Here are some follow up questions.

• How much does air resistance slow the dart down? Make an estimate based on the size and mass of the dart. If the dart was shot in a space station (so you could ignore gravitational effects), how far would it travel? What is the effective range of the dart?


• Projectile motion. If you neglect air resistance, how high will the dart travel if you shoot it straight up? How far horizontally will the dart travel if you shoot it from a standing position and aimed horizontally?


• Estimate the stretch distance and the spring constant for the spring inside the gun.

Some of those questions aren’t too difficult.

Other Holiday Homework Questions

Now that you have an example, here are some other questions.

1. Twist ties. For the past few years, it seems like many toys have been packaged with an increasing number of twist ties to hold them into the package.

Experimentally create a model for the retaining force strength as a function of twists. So, if you twist it twice instead of once, is it twice as strong?

2. Twist ties and time. Estimate the total amount of time (in human hours) that was spent in Christmas morning in the USA undoing twist ties.

3. Air drag and power. Here is a running parachute.

Running with a parachute.

Estimate the increase in power needed to run with the parachute.

4. Wrapping paper. Suppose you took all the wrapping paper used in the USA during Christmas. If you put all of this together (tape it together), how much surface area would it cover? Would it be enough to cover a city? What about Rhode Island? Could you see it from orbit?

5. Hot Christmas trees. Suppose you have normal incandescent bulbs on your Christmas tree. What perecent of the electrical power goes into thermal power? Does your tree actually get hot?

Thermal image of a Christmas tree.

This older post on the power used by Christmas lights might be helpful.

That’s your homework.

Machine Intelligence Cracks Genetic Controls

Every recipe has both instructions and ingredients. So does the human genome. An error in the instructions can raise the risk for disease.

Every cell in your body reads the same genome, the DNA-encoded instruction set that builds proteins. But your cells couldn’t be more different. Neurons send electrical messages, liver cells break down chemicals, muscle cells move the body. How do cells employ the same basic set of genetic instructions to carry out their own specialized tasks? The answer lies in a complex, multilayered system that controls how proteins are made.

Most genetic research to date has focused on just 1 percent of the genome—the areas that code for proteins. But new research, published Dec. 18 in Science, provides an initial map for the sections of the genome that orchestrate this protein-building process. “It’s one thing to have the book—the big question is how you read the book,” said Brendan Frey, a computational biologist at the University of Toronto who led the new research.

Frey compares the genome to a recipe that a baker might use. All recipes include a list of ingredients—flour, eggs and butter, say—along with instructions for what to do with those ingredients. Inside a cell, the ingredients are the parts of the genome that code for proteins; surrounding them are the genome’s instructions for how to combine those ingredients.

Just as flour, eggs and butter can be transformed into hundreds of different baked goods, genetic components can be assembled into many different configurations. This process is called alternative splicing, and it’s how cells create such variety out of a single genetic code. Frey and his colleagues used a sophisticated form of machine learning to identify mutations in this instruction set and to predict what effects those mutations have.

Olena Shmahalo/Quanta Magazine

The researchers have already identified possible risk genes for autism and are working on a system to predict whether mutations in cancer-linked genes are harmful. “I hope this paper will have a big impact on the field of human genetics by providing a tool that geneticists can use to identify variants of interest,” said Chris Burge, a computational biologist at the Massachusetts Institute of Technology who was not involved in the study.

But the real significance of the research may come from the new tools it provides for exploring vast sections of DNA that have been very difficult to interpret until now. Many human genetics studies have sequenced only the small part of the genome that produces proteins. “This makes an argument that the sequence of the whole genome is important too,” said Tom Cooper, a biologist at Baylor College of Medicine in Houston, Texas.

Reading the Recipe

The splicing code is just one part of the noncoding genome, the area that does not produce proteins. But it’s a very important one. Approximately 90 percent of genes undergo alternative splicing, and scientists estimate that variations in the splicing code make up anywhere between 10 and 50 percent of all disease-linked mutations. “When you have mutations in the regulatory code, things can go very wrong,” Frey said.

“People have historically focused on mutations in the protein-coding regions, to some degree because they have a much better handle on what these mutations do,” said Mark Gerstein, a bioinformatician at Yale University, who was not involved in the study. “As we gain a better understanding of [the DNA sequences] outside of the protein-coding regions, we’ll get a better sense of how important they are in terms of disease.”

Scientists have made some headway into understanding how the cell chooses a particular protein configuration, but much of the code that governs this process has remained an enigma. Frey’s team was able to decipher some of these regulatory regions in a paper published in 2010, identifying a rough code within the mouse genome that regulates splicing. Over the past four years, the quality of genetics data—particularly human data—has improved dramatically, and machine-learning techniques have become much more sophisticated, enabling Frey and his collaborators to predict how splicing is affected by specific mutations at many sites across the human genome. “Genome-wide data sets are finally able to enable predictions like this,” said Manolis Kellis, a computational biologist at MIT who was not involved in the study.

Etna Has First Intense Eruption in Over a Year

The glowing New Southeast Crater during the eruption of Etna on December 28, 2014. Image taken from video by Alessandro Lo Piccolo / YouTube.

It has been a quiet year for Italy’s Etna, but as if to remind everyone that the volcano is almost always ready to erupt, Etna produced its most intense eruption (“paroxysm” in the lingo of the Osservatorio Etneo) since December 2013. This eruption from the New Southeast Crater had all the classic pieces of an Etna eruption – lava fountains, lava flows and ash fall that covered the region with dark grey volcanic debris. However, as intense as it was, it was also brief, ending within a few hours of starting and by this morning, Etna was merely steaming in the morning sun (see below). You can check out some video of the eruption taken last night by Alessandro Lo Piccolo, where the ash-and-steam column is clearly seen glowing red (see above, likely reflecting the light from the lava fountains and lava flows).

The steaming crater of Etna seen on the morning of December 29, 2014, following the previous night’s paroxysm. Photo by Dr. Boris Behncke, used by permission.

Etna’s eruption is a great reminder that you still have 2 days to vote for the 2014 Pliny for Volcanic Event of the Year. Cast your ballot by December 31 to be counted!

Holiday Physics Homework

Rhett Allain

It’s that time of year. Christmas, New Years, and other holiday stuff. Now you can just sit around in your pajamas and watch football. Or can you? Don’t forget your holiday physics homework.

Before I post your homework, I am going to give you an example. If I don’t give an example, everyone gets angry. So here it is (yes, this is an old problem with new data).

How Fast Is That Nerf Dart?

Everyone loves Nerf guns. Also, if you borrow your wife’s phone you can easily make a slow motion video.

Slow motion video at 240 fps.

This is a 240 fps video from the iPhone 6 (here is a youtube version). It’s a little difficult to see, but there is also a meterstick on the ground for scaling. You should know what comes next – video analysis with Tracker Video Analysis. I’ll just skip all the details (but here is a quick video analysis tutorial) and go straight to a plot of the position of the dart.

Since the dart was shot at an angle, I have included plots for both the x- and y-position. Looking at the slope, this gives an x-velocity of 19.2 m/s and a y-velocity of 3.04 m/s. This gives an average magnitude of 19.44 m/s. This speed is quite a bit faster than this other Nerf gun I tested at around 10 m/s.

See. That’s not so difficult of a homework problem. Actually, you could take this one step farther. Here are some follow up questions.

• How much does air resistance slow the dart down? Make an estimate based on the size and mass of the dart. If the dart was shot in a space station (so you could ignore gravitational effects), how far would it travel? What is the effective range of the dart?


• Projectile motion. If you neglect air resistance, how high will the dart travel if you shoot it straight up? How far horizontally will the dart travel if you shoot it from a standing position and aimed horizontally?


• Estimate the stretch distance and the spring constant for the spring inside the gun.

Some of those questions aren’t too difficult.

Other Holiday Homework Questions

Now that you have an example, here are some other questions.

1. Twist ties. For the past few years, it seems like many toys have been packaged with an increasing number of twist ties to hold them into the package.

Experimentally create a model for the retaining force strength as a function of twists. So, if you twist it twice instead of once, is it twice as strong?

2. Twist ties and time. Estimate the total amount of time (in human hours) that was spent in Christmas morning in the USA undoing twist ties.

3. Air drag and power. Here is a running parachute.

Running with a parachute.

Estimate the increase in power needed to run with the parachute.

4. Wrapping paper. Suppose you took all the wrapping paper used in the USA during Christmas. If you put all of this together (tape it together), how much surface area would it cover? Would it be enough to cover a city? What about Rhode Island? Could you see it from orbit?

5. Hot Christmas trees. Suppose you have normal incandescent bulbs on your Christmas tree. What perecent of the electrical power goes into thermal power? Does your tree actually get hot?

Thermal image of a Christmas tree.

This older post on the power used by Christmas lights might be helpful.

That’s your homework.

Machine Intelligence Cracks Genetic Controls

Every recipe has both instructions and ingredients. So does the human genome. An error in the instructions can raise the risk for disease.

Every cell in your body reads the same genome, the DNA-encoded instruction set that builds proteins. But your cells couldn’t be more different. Neurons send electrical messages, liver cells break down chemicals, muscle cells move the body. How do cells employ the same basic set of genetic instructions to carry out their own specialized tasks? The answer lies in a complex, multilayered system that controls how proteins are made.

Most genetic research to date has focused on just 1 percent of the genome—the areas that code for proteins. But new research, published Dec. 18 in Science, provides an initial map for the sections of the genome that orchestrate this protein-building process. “It’s one thing to have the book—the big question is how you read the book,” said Brendan Frey, a computational biologist at the University of Toronto who led the new research.

Frey compares the genome to a recipe that a baker might use. All recipes include a list of ingredients—flour, eggs and butter, say—along with instructions for what to do with those ingredients. Inside a cell, the ingredients are the parts of the genome that code for proteins; surrounding them are the genome’s instructions for how to combine those ingredients.

Just as flour, eggs and butter can be transformed into hundreds of different baked goods, genetic components can be assembled into many different configurations. This process is called alternative splicing, and it’s how cells create such variety out of a single genetic code. Frey and his colleagues used a sophisticated form of machine learning to identify mutations in this instruction set and to predict what effects those mutations have.

Olena Shmahalo/Quanta Magazine

The researchers have already identified possible risk genes for autism and are working on a system to predict whether mutations in cancer-linked genes are harmful. “I hope this paper will have a big impact on the field of human genetics by providing a tool that geneticists can use to identify variants of interest,” said Chris Burge, a computational biologist at the Massachusetts Institute of Technology who was not involved in the study.

But the real significance of the research may come from the new tools it provides for exploring vast sections of DNA that have been very difficult to interpret until now. Many human genetics studies have sequenced only the small part of the genome that produces proteins. “This makes an argument that the sequence of the whole genome is important too,” said Tom Cooper, a biologist at Baylor College of Medicine in Houston, Texas.

Reading the Recipe

The splicing code is just one part of the noncoding genome, the area that does not produce proteins. But it’s a very important one. Approximately 90 percent of genes undergo alternative splicing, and scientists estimate that variations in the splicing code make up anywhere between 10 and 50 percent of all disease-linked mutations. “When you have mutations in the regulatory code, things can go very wrong,” Frey said.

“People have historically focused on mutations in the protein-coding regions, to some degree because they have a much better handle on what these mutations do,” said Mark Gerstein, a bioinformatician at Yale University, who was not involved in the study. “As we gain a better understanding of [the DNA sequences] outside of the protein-coding regions, we’ll get a better sense of how important they are in terms of disease.”

Scientists have made some headway into understanding how the cell chooses a particular protein configuration, but much of the code that governs this process has remained an enigma. Frey’s team was able to decipher some of these regulatory regions in a paper published in 2010, identifying a rough code within the mouse genome that regulates splicing. Over the past four years, the quality of genetics data—particularly human data—has improved dramatically, and machine-learning techniques have become much more sophisticated, enabling Frey and his collaborators to predict how splicing is affected by specific mutations at many sites across the human genome. “Genome-wide data sets are finally able to enable predictions like this,” said Manolis Kellis, a computational biologist at MIT who was not involved in the study.

Out-of-Print Games We Were Thrilled to Play Again in 2014

Mighty Final Fight

How did Capcom turn Final Fight, a gritty, risque arcade game about street violence, into a cartoonish kid-friendly comedy? Mighty Final Fight has super-kawaii, ultra-chibi versions of Cody, Haggar and Guy roaming around Metro City and punching their equally adorable opponents to death. VGMuseum/Capcom

Mighty Final Fight

How did Capcom turn Final Fight, a gritty, risque arcade game about street violence, into a cartoonish kid-friendly comedy? Mighty Final Fight has super-kawaii, ultra-chibi versions of Cody, Haggar and Guy roaming around Metro City and punching their equally adorable opponents to death. Light role-playing game elements make this more than your average brawler. And the original NES cartridge is quite expensive these days, so we're happy to have this in cheap download form on both Wii U and 3DS.

VGMuseum/Capcom

X-Wing and TIE Fighter

Fight with the Rebel Alliance, or join the Empire? This pair of classic Star Wars interstellar dogfight games haven't been seen since the days of floppies and CD-ROM. We're still wondering what Disney will do with Star Wars movies, but it sure is being great about giving us classic Star Wars gaming to bide our time with. Disney

X-Wing and TIE Fighter

Fight with the Rebel Alliance, or join the Empire? This pair of classic Star Wars interstellar dogfight games haven't been seen since the days of floppies and CD-ROM. We're still wondering what Disney will do with Star Wars movies, but it sure is being great about giving us classic Star Wars gaming to bide our time with.

Disney

Demon's Crest

Don't you hate that a-hole red devil guy from Ghosts N' Goblins? Play this and you'll love him. Demon's Crest is the sequel to the Gargoyle's Quest games for Game Boy and NES (both of which are also available through download on Nintendo 3DS), and it's a non-linear platforming game with RPG elements. Capcom

Demon's Crest

Don't you hate that a-hole red devil guy from Ghosts N' Goblins? Play this and you'll love him. Demon's Crest is the sequel to the Gargoyle's Quest games for Game Boy and NES (both of which are also available through download on Nintendo 3DS), and it's a non-linear platforming game with RPG elements.

Capcom

Vib-Ribbon

From the creator of the acclaimed early music game Parappa the Rapper comes this no-longer-forgotten PlayStation classic. It's a simple beat-matching game---a wireframe vector-graphics rabbit runs along a simple white line on a black background, and you dodge obstacles by tapping buttons to the beat. Sony

Vib-Ribbon

From the creator of the acclaimed early music game Parappa the Rapper comes this no-longer-forgotten PlayStation classic. It's a simple beat-matching game---a wireframe vector-graphics rabbit runs along a simple white line on a black background, and you dodge obstacles by tapping buttons to the beat. The trick is, you can insert an audio CD and use your own music. You can only use that functionality on the PlayStation 3 re-release. If you play it on your PSP or PS Vita, you can only play the included, original tracks (which are adorable).

Sony

Metroid Fusion

If you've never played Super Metroid, a deep-space action-adventure that's a strong candidate for one of the best games ever made, get it on your Wii U now. If you have played it, and want more, get the sequel Metroid Fusion . Nintendo

Metroid Fusion

If you've never played Super Metroid, a deep-space action-adventure that's a strong candidate for one of the best games ever made, get it on your Wii U now. If you have played it, and want more, get the sequel Metroid Fusion . Originally released on the Game Boy Advance, you can now play it on your giant TV via Nintendo's Wii U. It looks surprisingly good blown up, like a 16-bit game that never happened.

Nintendo

Tomba! 2

Weirdly, Sony's been unable to get the English-language version of this PlayStation classic working on modern consoles due to some strange emulation issues. But the Japanese version works, so MonkeyPaw Games brought it over. Monkey Paw Games

Tomba! 2

Weirdly, Sony's been unable to get the English-language version of this PlayStation classic working on modern consoles due to some strange emulation issues. But the Japanese version works, so MonkeyPaw Games brought it over and posted a helpful walkthrough on its website to get you past the fact that you can't understand what it's trying to tell you. Stick it out and you'll find a funny, quirky puzzle-platform game; they don't make 'em like this anymore.

Monkey Paw Games

Yoshi's Island: Super Mario Advance 3

Nintendo loves re-releasing Mario games, but one of the best ever, Yoshi's Island, hasn't been seen since its initial release on Super Nintendo. But the Game Boy Advance version of the game---basically the same game, but with a whole bunch of minor and arguably major changes---is available on Wii U's Virtual Console. Nintendo

Yoshi's Island: Super Mario Advance 3

Nintendo loves re-releasing Mario games, but one of the best ever, Yoshi's Island, hasn't been seen since its initial release on Super Nintendo. This holds true even today---it may be issues emulating the Super FX co-processor on the cartridge. But the Game Boy Advance version of the game---basically the same game, but with a whole bunch of minor and arguably major changes---is available on Wii U's Virtual Console. Sequels to this game also let you play as the dinosaur Yoshi, eating fruit, pooping eggs and throwing them at anything that annoys you. But it's never been as good as the first time.

Nintendo

Suikoden II

This classic role-playing game from Konami has long been one of the most sought-after PlayStation discs. You can still expect to pay over $100 for the original, but why bother when you can download it on PlayStation 3, PSP and Vita? Konami

Suikoden II

This classic role-playing game from Konami has long been one of the most sought-after PlayStation discs. You can still expect to pay over $100 for the original, but why bother when you can download it on PlayStation 3, PSP and Vita? Jason Schreier at Kotaku called it "Pokemon meets Game of Thrones"---a blend of well-written dramatic story and addictive collect-em-all mechanics in which you have to recruit an army of characters to your side as you play through the game. That guy in the item shop might be a valuable asset to your team, if you can convince him to join up!

Konami

Strider 2

Buy Strider 2 for the PlayStation Store and you can experience two full games: The arcade original Strider and its 1999 sequel, released in arcades in Japan but mostly known for the PlayStation version released shortly thereafter. Capcom

Strider 2

Capcom's kinetic arcade classic about a future-ninja with an awesome sword got a great next-generation version earlier this year. Buy Strider 2 for the PlayStation Store and you can experience two full games: The arcade original Strider and its 1999 sequel, released in arcades in Japan but mostly known for the PlayStation version released shortly thereafter. It doesn't take too long to credit-feed your way through both of these arcade ports and finish them, but you'll have a blast while they last.

Capcom

Sam & Max Hit the Road

Telltale Games has produced three seasons of episodic adventure games starring Steve Purcell's violent, hilarious dog and rabbit detectives. But the game that started it all, a LucasArts classic from 1993, hasn't been available digitally until now. Disney

Sam & Max Hit the Road

Telltale Games has produced three seasons of episodic adventure games starring Steve Purcell's violent, hilarious dog and rabbit detectives. But the game that started it all, a LucasArts classic from 1993, hasn't been available digitally until now. If we're being honest, the humor is sharper and the voice acting is snappier than the Telltale sequels. A brilliant, ridiculous plot about a Bigfoot chase across the United States still holds up today. It does have some impossible-without-a-hint-book puzzles, so feel free to use the digital strategy guide included with the download at Good Old Games.

Disney

All of the Castlevanias

All three Castlevania games for Game Boy Advance are now available on Wii U's eShop, including Circle of the Moon and Harmony of Dissonance (pictured). If you only buy one, get Aria of Sorrow ---it's the best by far. Nintendo

All of the Castlevanias

All three Castlevania games for Game Boy Advance are now available on Wii U's eShop, including Circle of the Moon and Harmony of Dissonance (pictured). If you only buy one, get Aria of Sorrow ---it's the best by far. Explore a massive, non-linear castle, throwing holy water and other assorted weaponry at werewolves and vampires and all sorts of other unholy nasties. Gorgeous pixel graphics and soundtrack round out the package. As with Metroid Fusion, the Game Boy graphics look pretty darn good even blown up to giant TV size.

Nintendo

Duck Hunt

Everybody had Duck Hunt on their NES. Everybody hated that stupid dog who laughed every time you missed a duck. Everybody put their Zapper gun flush against their television tube to hit the ducks at point-blank range. VGMuseum/Nintendo

Duck Hunt

Everybody had Duck Hunt on their NES. Everybody hated that stupid dog who laughed every time you missed a duck. Everybody put their Zapper gun flush against their television tube to hit the ducks at point-blank range. Sadly, that Zapper gun won't work with your flatscreen. But Nintendo's emulated the classic for Wii U, and it works with your Wiimote. Now that the Duck Hunt bird and dog are playable characters in the new Super Smash Bros., it's high time their original classic came back.

VGMuseum/Nintendo

This year brought us a lot of great new games. And we probably ignored a lot of them for these old games.

The spread of digital distribution platforms on PCs and game consoles has brought us not only innovative, low-budget indie games, but a new home for classic out-of-print titles. Nintendo’s Virtual Console on its Wii U and 3DS has brought back classics from Super Nintendo, Game Boy and more for a few bucks each. Sony’s PlayStation Network hosted fewer games this year, but some of them were very expensive to track down on CD-ROM. On PC, services like Steam and Good Old Games added more classic computer games to their growing archives.

Here are the games, long out of print, that we were thrilled to see make a digital comeback in 2014.

View the gallery in full screen mode for more information and bigger, blockier pixels.