Sequencing a Single Chromosome

In the last three years, the number of human genomes that have been sequenced (their DNA read letter by letter) has jumped from a handful to hundreds, with thousands more in progress. But all of those genome readings lack some crucial information. A person inherits two copies of each chromosome, one maternally and one paternally. Existing sequencing methods do not indicate whether genetic variations that lie close to each other on the genomic map were inherited from the same parent, and therefore come from the same chromosome, or if some lie on the maternal chromosome and some on the paternal one. Knowing this has a variety of uses, from sequencing fetal DNA to more easily detecting the genes responsible for different diseases to better tracking human evolution.

Now two teams have devised ways to determine these groupings?known as the haplotype?in an individual. Stephen Quake and collaborators at Stanford University developed a way to physically separate the chromosome pairs and sequence each strand of DNA individually. Jay Shendure and colleagues at the University of Washington in Seattle sequenced DNA from single chromosomes in specially selected pools and used this information to piece together the genome. Both projects were published this week in Nature Biotechnology.

"It was a real technical flaw in the genomes [sequences] that have been published to date," says Quake, a bioengineer at Stanford who was one of Technology Review's top innovators under 35 in 2002. "Every genome we are going to do from now on going will be recorded with the haplotype."

Quake's team capitalized on microfluidics technology that they have developed for separating and analyzing single cells. First, the researchers trapped single cells during a specific phase of the cell cycle in which the two copies of its chromosomes are split apart. Then they burst open the cell, randomly partitioned chromosomes into different chambers on a microfluidics chip, and copied, or amplified, and analyzed the DNA in each chamber.

Shendure, a TR35 winner in 2006, and his team amplified 40,000 letter stretches of DNA randomly sampled from individual chromosomes. Because each piece of DNA comes from one half of a chromosome pair, researchers know that all the genetic variants within its sequence lie on the same chromosome.

Shendure and Quake say that having haplotype information will have an enormous impact on human genetics, helping not only to diagnose and understand the genetic basis of some diseases but also to track the evolution of our species from primate ancestors.

If someone has two disease-linked mutations within a single gene, it's difficult to determine with current genome sequencing methods if there is one genetic mistake on the maternal copy and one on the paternal copy or if both variations lie within the same copy of the gene. In the former case, the person has two defective genes, which are likely to cause health problems. In the latter, the person has one good copy of the gene and one bad copy. In many cases, having the good copy can compensate for the defective one.

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10 Last Minute Gifts for Mobile Geeks [TNW Mobile]

Cinema Seat

Cinema SeatThe Cinema Seat iPad accessory aims to make long car rides with the kids more enjoyable. It simply enables the iPad to fit on the back of the car seat by the use of stretchable straps that fit around the headrest.

There are several reasons this is a good idea. First off, depending on the age of the child, it might not be the best idea to let them mess with the iPad. The idea of possible spills, scratches or the deletion of documents would make any iPad user cringe ?this accessory makes the iPad hands-off. Also, if there?s more than one person in the backseat, someone would be stuck holding it on their lap but with Cinema Seat, the iPad is nicely positioned at eye level. The backseat case additionally holds small accessories in its pocket and still allows users to access iPad connector and controls. It?s priced at $39.99.

Foodie iPhone Cases ? Like Bacon?

Bacon CaseSure, these accessories are a bit strange but they?re perfect for foodie-iPhone nut in your life. Strapya cases are available in a variety of unique styles including; bacon & eggs, sushi, spaghetti, hashbrowns, chocolate ?even Christmas cake. The bacon & eggs design is my personal favourite but they?re all brilliant and appear to be very realistic. One thing?s for sure, if you buy one of these cases, there?s a pretty good chance the recipient of the gift doesn?t already have one. The Strapya cases are between $40-$47.

GorillaPod for iPhone & iPod Touch

GorillaPodThe entire line of GorillaPod accessories are used stabilize devices such as cameras, fiipcams and iPhones. The GorillaPod is a tripod supported by three legs however it?s different from standard tripods because the legs are bendy and can be wrapped around and hung from objects, a perfect fit for the ?guerilla? style videographer. There are tons of possible uses for this accessory but podcasting (by yourself) is probably the best example because it can be a difficult task to film yourself. Podcasters could easily shoot a video of themselves by attaching the device to a pole or tree and it completely eliminates the need for someone to hold the device while filming. There are different models available for iPhone 4, 3G, 3GS and the iPod touch. The GorillaPod iPhone 4 tripod comes with a bonus clip and a universal camera adapter clip with a º-20 screw. Depending on the iPhone, the prices range between $29.99- 39.99.

Bringrr

Do you know someone who constantly leaves their phone at home? Bringrr is a Bluetooth accessory that fits into the car?s power socket and is capable of telling you when you forgot your device. When you start the car, Bringrr will immediately start searching for the device over Bluetooth and if it can?t find the device, it notifies the user that the device is out of range. Aside from reminding users to grab their devices, the Bringrr Charge model also charges the battery while the Bringrr Classic is limited to acting as a ?device reminder?.Bringrr is available in 2 different versions; iPhone and Micro USB (Android). The models are $29.95- $39.95 and it works will almost all Bluetooth enabled devices.

Scosche KickBACK P1 iPad Case

iPad CaseIf there?s someone on your shopping list getting the iPad, Scosche?s KickBACK P1 case is a great gift for ensuring its protection. The case is made of shatterproof polycarbonate and shock resistant rubber coupled with traction nubs and a kickstand that props the iPad up in both landscape and portrait modes ? perfect for lying back and watching media. Using a shockproof case is ideal for accidental falls. An accessory I?d definately throw on before handing the iPad over to my accident-prone nephew. The positioning of the kickstand located on the back is also handy for typing as it can be adjusted for low angle typing. The KickBACK P1 comes in solid black and costs $59.99.

iTrip DualConnect (Car charger + FM Transmitter)

iTrip DualConnectorThe iTrip DualConnect gadget accessory is an FM transmitter and iPhone & iPod touch battery charger in one. The FM transmitter part of the accessory will broadcast your device?s music over FM frequency, so users can listen to their device?s library through the car stereo. It plugs into the car?s 12 volt power outlet allowing the iPhone/iPod touch to charge through a dock connector that attaches to iTrip. Setting it up appears to be very simple with the use of their free companion iOS app. Using iTrip?s app, the car radio is tuned while adjusting the signal levels to achieve a high quality sound. This accessory provides and AUX jack as well, giving users a way to transmit the signal directly through an AUX port. Skipping a song, pressing pause or hitting stop during a song is possible through play/pause/forward/back controls located on the front of the device. Griffin?s iTrip DualConnect is $59.99, not a bad price considering you get two accessories in one.

Powermat 2X Portable Mat & Powercube

PowermatThe Powermat 2X Portable Mat is a great gift for mobile gadget nuts because it allows users to charge multiple devices without the need of a power outlet. It sports a built-in rechargeable high capacity battery that gives the devices a charge, and it supports up to 4 charges for most devices. To use the Powermat, users simply drop their devices on the mat and it magically starts charging. This specific model of Powermat is equipped with a powercube that lets users charge tons of different devices with the use of tips. Multiple devices become compatible after the user attaches one of 8 tips to the gadget they wish to charge. Powermat 2x additionally comes with a power supply to charge the rechargeable battery. When the charging is finished, the powermat nicely folds up and fits into the provided carrying case. It?s available for $129.99.

Multi-Touch Gloves

GlovesSadly, the multi-touch displays of the iPhone, iPad and Android don?t work if you?re wearing gloves. And, ripping off the gloves in zero below weather to simply check your phone, can be seriously annoying if not a painful task. However, there are quite a few brands making multi-touch supported gloves that solve this issue. One of my favourite pairs are called the North Face E-Tip. These gloves don?t have any other special features aside from working with the touch screen but the design looks ultra-techy and they seem to be thin enough for proper typing. As we?d mentioned, there are several types of these gloves available including; Dot gloves, Tavo gloves and free hands gloves. Overall, a pair of multi-touch supported gloves is a thoughtful gift idea for mobile obsessed friends and family.

HD Anti-Glare Film for iPad

Anti-GlareThis Anti-Glare film accessory is a protective sheet of plastic that fits on the screen of the iPad. The plastic was designed to reduce glare, fingerprints, dust and smudges while giving users a higher detail of sheet to view the screen through. The sheet sticks to the screen using static which avoids leaving behind any gross/ sticky residue. $34.95 might be a lot to pay for a single sheet of plastic but scratching a $600 iPad is far worse than dropping $35. I?m sure any iPad user who receives a screen-protecting accessory will be very thankful.

Pinball Magic & JackPot Slots

Newpotatotech have designed series of accessories that can turn your iPhone into either a slot or pinball machine.

Pinball Magic
Pinball MagicPinball Magic
aims to recreate the tactile arcade experience with a working mini pinball case that fits around the iPhone by connecting to the standard 30pin connector. This accessory is similar to real pinball machines and sports a rotating beacon light, animated LED light score board, ball launcher, flipper buttons, credit/select buttons and has folding table legs. Pinball Magic works with a free app available in the app store however, it?s posted on Newpotatotech?s site that it will support additional third-party pinball apps very soon.
The game-play offers a few different modes and layouts; multi-player (support up to 4 players), tilt detection, end of ball, replay bonuses and various multi-ball modes. This case supports the iPhone 4 or any iPhone and iPod touch.

JackPot Slots

JackPot SlotsThe iPhone fits into the JackPot Slot case in the same way as Pinball Magic but this one will sync and charge the iPhone. Think of this like a tricked-out charge and sync dock for the device. It comes with a USB charging cable for charging along with an arm that turns the iPhone into a one-armed bandit. The JackPot Slot works with an iOS app that gives users lots different slots games at different levels of difficulty ? you can even win real prizes. Once a user accumulates 50,000 in credits, they are entered in a draw at Newpotatotech and have the chance to win weekend getaways and other select prizes. Both Pinball Magic and JackPot Slots work with the iPhone and iPod touch and are available for $79.99

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Source: http://thenextweb.com/mobile/2010/12/22/10-last-minute-gifts-for-mobile-geeks/

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The Chrome Web Store is broken and it?s not Google?s fault [TNW Google]

It?s been a few weeks since we first got the announcement about the Chrome Web Store. That means that it?s time to revisit and figure out whether or not Google is really onto something big with its invention.

But the Web Store is broken. Not because of Google ? at least not in full ? but more because developers simply aren?t looking at its full potential.

The question that was asked, and I think that it?s the one that still remains, is whether the Web Store really solves a problem that already exists. While many of us on the front-facing side of technology do appreciate the move toward a cloud society, there is still a huge group of people who either don?t trust the cloud or don?t see a reason for it.

After the first day of using a few applications downloaded via the Web Store, I was already seeing my patterns shift. The real problem that I?ve found, like so many others on the store, is that many developers and/or sites just aren?t taking full advantage of the Chrome browser platform. There are a number of ?apps? that are nothing more than handy links to another site. The notable exception, of course, being ChromeDeck.

TweetDeck on the Chrome browser is a thing to behold. It?s slick, it?s fast and it?s just about as powerful as the vast majority of people would ever need. Though it does employ user streams, it?s not dead-on real-time, but it?s really close. The best part? It?s not some off-machine website. Everything in TweetDeck for Chrome is rendered natively in the browser, taking full use of the application?s ability to host other applications.

TweetDeck on Chrome is something that honestly does solve a problem. For those of use who use TweetDeck as our main Twitter client, dealing with the frustrations of the laggy Adobe Air platform is a pain. ChromeDeck solves this, with an HTML5 interface. While website-based ?applications? might be slick looking, they don?t really provide anything that isn?t available in any other browser.

Is the lack of necessity to use web apps really the fault of Google? On one hand, yes. Google could, in the same way that Apple does with the App Store, regulate that applications in the Chrome Web Store have to be somehow enhanced to run on Chrome. Is that fair to the rest of the world? Not really, but we?re not talking about fairness here. We?re talking about solving problems.

The other side of the coin is that Google isn?t at fault simply because the developers haven?t delved deeply enough into the Chrome architecture to take advantage of it. TweetDeck did, and out of it came an amazing product that won?t run on other browsers. Pretty much every other impressive application that I?ve used, though, runs just as well on Safari, Firefox and even some in Internet Explorer.

So has my behavior shifted? Yes, somewhat. In that case, the Web Store is working just fine. However, I?m still reliant heavily on apps to the point that I can?t use my Cr-48 for a full-day jaunt. I tend to look for apps more than I do sites. Or at least I tend to look for apps of sites that I like. I also appreciate the doors that will open in the future as more sites continue to migrate over to an app culture.

The problem isn?t fully solved, but it also doesn?t fully exist. The Web Store, as it stands, is a broken idea that holds a huge amount of potential. It?s up to the developers, however, to realize that potential. As the saying goes, you can lead a horse to water?

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Source: http://thenextweb.com/google/2010/12/22/the-chrome-web-store-is-broken-and-its-not-googles-fault/

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HP to unveil three webOS tablets at CES?

HP is among the dozens of manufacturers planning to ship consumer tablets next year, and rumor has it that the company will introduce three models during CES 2011. Citing a "trusted source," Fox News reports that all three will run webOS 2.5.1 and describes them as a "spin-off" of the enterprise-focused Windows-based Slate 500, which launched in October after being delayed.

HP's upcoming slates feature rounded edges and are supposedly thinner and lighter than Apple's iPad (1.25 pounds versus 1.5 to 1.6 pounds). Features include Sprint 4G connectivity, mini-HDMI and USB 3.0 ports, as well as two cameras with LED flash (1.3MP in the front, 3MP in the back). At least one slate will have a 9.7-inch display that is "nearly identical" to the iPad's.


The company is also said to be developing a fourth tablet for academic use, but it won't be ready for CES. It sounds like the universities will be able to custom order this model, which sports an 8.9-inch screen and will give students to access the school's internal educational software. HP reportedly plans to ship the academic slate by fall 2011, while the others are due in March.

We all know HP has consumer tablets up its sleeve, but whether they'll appear at CES 2011 is another story. Engadget notes that the company hasn't emailed press invitations to an HP/Palm shindig at CES, and the company usually sends notifications earlier than mid-December -- not to mention that HP has arranged a smaller floor presence this year than previous years.

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Source: http://www.techspot.com/news/41683-hp-to-unveil-three-webos-tablets-at-ces.html

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What is on that screen?

What is on that screen?

Posted on 18th Dec 2010 at 12:30 by James Gorbold with 88 comments

One of the first things I do when proof reading an article that is about to be published on bit-tech or Custom PC is check whether the URL at the top of the review does correctly link to the product manufacturer's homepage.

So while proofing the review of the MSI X58A-GD65 motherboard I came across this image which I just had to share with you. It's an advert admitedly, but the artwork is so bizarre that I thought it worth a caption competition.

What is on that screen? *What is on that screen?

To get things started, this is what some of the bit-tech/CPC editorial's team suggestions:

1. MSI has installed fans in the screen.

2. He's just seen a video of his parents having sex.

3. He's just seen the first benchmarks of a LGA2011 CPU.

Over to you...

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Roku CEO: Apple TV launch helped boost Roku sales

Roku has been selling inexpensive Internet TV set-top boxes since 2008, when it was only streaming on-demand content from Netflix, and has since diversified its offerings in terms of hardware and content. Reviews and customer response has been mostly positive but its devices have yet to reach mainstream status. Youd think that with Apple and Google making big moves into the segment this year Roku would be taking a big hit, but apparently thats not the case at all.

According to Roku CEO Anthony Wood, the introduction of the Apple TV has helped raise awareness of the entire market, more likely because of all the attention Apples every move gets from the media rather than for the product itself, and at the same time this has helped consumers realize some of Rokus advantages over its rivals -- such as the ability to play 1080p content with the $100 Roku XDS player from a variety of sources, including Hulu Plus.


Wood points out that Roku will probably have sold its millionth set-top box by the end of the year, cracking $50 million in revenue, and the company expects to top $100 million in sales next year. Amazon is a significant factor in Roku sales, contributing about 25%, with the Roku XD and XDS among the top-selling devices in the sites electronics category.

Looking forward the executive says next year theyll continue to push for broader retail distribution, offer more products via licensing deals (such as the new Netgear Roku device), and bring more content to its devices. But competition will only get harder with Apple expected to launch an App Store for Apple TV, Google TV getting some refinements and a bunch of hardware partners, and gaming consoles catching on as an entertainment devices.

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Source: http://www.techspot.com/news/41668-roku-ceo-apple-tv-launch-helped-boost-roku-sales.html

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FCC set to vote on net neutrality rules today

The U.S. Federal Communications Commission is set to vote on a set of regulations designed to ensure that Internet providers treat all types of web content equally. The "net neutrality" rules, pushed by FCC Chairman Julius Genachowski, would mark the government's biggest move yet in what has been a contentious debate between companies providing access to the web and consumer groups advocating for an open Internet.

Essentially the new rules would theoretically keep service providers from charging differentiated fees for different types of content or slowing down certain websites or apps -- those belonging to a competitor, for example while discouraging but not expressly forbidding faster transmission of data from high-paying clients. If it passes, as it is expected to do with three votes against two, the plan will go before Congress for final approval.

Two Democratic commissioners voting in favor of the proposition, Michael Copps and Mignon Clyburn, acknowledged that the order was not as strong as they would have liked but are letting it move forward hoping it can be tweaked later. One of their main concerns is that the rules for wireless carriers are not strong enough it includes transparency requirements on network management policies and a basic "no-blocking" that covers websites, but not applications or services unless those applications directly compete with providers voice and video products, like Skype or Vonage.

This half-measure approach would mean that wireless carriers could indeed block or charge more for other types of Internet applications, such as video or social networking services, which is particularly worrying after seeing some recently leaked slides that show carriers are at least considering to go this route. FCC officials claim there are technological reasons for the wireless distinctions, and that they would continue to closely monitor the medium.

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Source: http://www.techspot.com/news/41667-fcc-set-to-vote-on-net-neutrality-rules-today.html

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Traktor Duo: Have an aspiring DJ on your list? Get them playing, for cheap. [TNW Apps]

Let?s start with some background ? I?ve been a DJ, behind turntables, for nearly 17 years. In that time, I?ve seen trends, fads and the things that have stuck around. As the lowly Technics 1200 turntable is seeing the end of its days, the age-old wisdom of ?learn to play vinyl first? just isn?t so fitting anymore.

What, then, should a budding DJ or even music fanatic do? There are a lot of options out there, and we?ll talk about quite a few of them. But one that absolutely needs to be on your radar is the Traktor Duo system from Native Instruments.

NI [Native Instruments] has been around for a long time. The company has learned some hard lessons over the years and has come out smelling like roses. In a market where DJ software runs the gamut from free to ?OH MY GOD? expensive, NI has found a great niche selling quality software at a price that won?t break your bank.

Traktor Duo is the entry-level offering from NI. It?s, simply, an installed software MP3 player for the Windows or OS X platform that will allow you to adjust speed, add effects, play with filters and mix music all in real time.

So what?s inside? Let?s take a look:

This is the basic interface of Traktor Duo. When you first load the software, then point it to a directory where you store your music, this is what you?ll see. Of course, you can choose to show or hide nearly any section of this screen, and resize it to your liking. But for this purpose, we?ll just have you look at what it is out of the box.

Up top, you see two ?decks?, left and right. Each one plays a track. Within each deck, you have options to match their tempo, add cue (starting) points, adjust the mapping (where the beats show up, in a track) and more. So, load up a track in the left side and, as long as y0u?ve spent a few seconds mapping out your tracks correctly, you can choose to Sync the right side and the tracks will play with the beats matching each other.

Organization of your tracks, in the bottom pane, is really simple. You can choose any number of features by which you want to sort, add and remove data at any time and add or remove any number of display options. The left side serves somewhat like a collection of crates, by which you can organize playlists, explore your files and check history.

Traktor Duo handles a wealth of formats: MP3, WAV, AIFF, Audio-CD, FLAC, Ogg Vorbis, non-DRM WMA (when running in Windows) and non-DRM AAC. That means that pretty much anything in your existing collection is now able to be played, manipulated and tweaked to your ear?s content.

What?s it feel like? Honestly, it feels a lot like what you?d be doing if you were playing records, just without the records. Though almost everything is controlled by mouse or button push, the premise is still the same. You load a track, wait for the appropriate time to start it, then let it roll while tweaking the sound with the effects. Traktor Duo is fluid, snappy and solid. The software has never once felt like it was on the edge of a crash and I?ve never had issues with latency even on older, lower-powered computers.

Now, is this the best way to learn how to DJ? Not really. Ideally speaking, every DJ would be able to mix tracks by their ears only, without visual cues. But, as I said before, that era is closing quickly. So, if you?ve got a visual learner on your hands, Traktor Duo is an inexpensive way to get them playing, while learning the ins and outs of what makes a mix sound good or bad.

Here?s the catch ? with just the software, you?ll not be able to fully use an external mixer. Fortunately, there?s an inexpensive solution to this in Traktor?s Audio 2 DJ sound card. It?s an external, USB-powered device that offers 2 sets of outputs so you can hook up a 2-channel mixer. The sound quality is, frankly, astounding given its price point of $119.

Want an even better deal? Traktor Duo normally runs $119 as well. Right now, there?s a 50-percent discount happening, so you can pick up the Audio 2 DJ plus Traktor Duo for less than $200 combined.

If you?re asking my opinion, that?s a pretty solid setup for the beginner DJ, for way less money than you?d ever have been able to pay in the past. Kudos to NI for the half-off deal, and for seeing the way that DJ?ing is changing. Have more in-depth questions? I?ve been a Traktor Scratch Pro user for almost 2 years. Fire away and I?ll answer anything I can.

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Source: http://thenextweb.com/apps/2010/12/21/traktor-duo-have-an-aspiring-dj-on-your-list-get-them-playing-for-cheap/

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Blog - Early Astronomer Described Coriolis Effect Centuries Before Coriolis

In the century or so after Copernicus proposed the modern view of the Solar System, theologians and scientists lined up to criticise the theory.

Chief among them was Giovanni Battista Riccioli, an Italian Jesuit priest and an astronomer himself of some renown. Riccioli was one of the first astronomers to map the Moon, giving names to many craters that we still use to today. He was also the first to measure the rate at which objects fall.

Riccioli's opposition to the heolicentric theory was not entirely dogmatic. He admired the Copernican hypothesis for its simplicity and even named one of the Moon's craters for Copernicus.

But Riccioli believed he had good reason to dismiss Copernicus' ideas. In 1651, in an encyclopedic work on astronomy called Almagestum Novum, he published 77 reasons why Copernicus was wrong.

Today, Christopher Graney at Jefferson Community & Technical College in Louisville, Kentucky, publishes a translation of some of these arguments (the originals are in latin).

It turns out that Riccioli's thinking was ahead of its time. One central Copernican hypothesis is that the Earth must rotate, to explain night and day. Riccioli dismisses this with the following line of thought.

Imagine a canon at the equator, firing canon balls towards the north pole. If the Earth rotates, the equator is moving faster than the pole. So any canon ball launched from the equator would pass over slower moving parts of the sphere to get to the pole. The result would be the canon ball veering off course.

Riccioli argues that because this does not happen, the Earth cannot be rotating.

That's a powerful argument. And Riccioli is entirely correct--the absence of this effect would be good evidence that the Earth is not rotating.

But as Graney points out, Riccioli is describing the Coriolis effect, an effect that influences motion in any rotating frame of reference. What Riccioli didn't realise, of course, is how small this effect is.

Today, we know that the Coriolis effect plays all kinds of subtle roles on Earth, not least of which is in influencing the motion of weather systems. And today, gunners do take this force into account when calculating trajectories.

But here's the thing: Gustave Coriolis, the French mathematician after whom the force is named, did his work on the subject in the 19th century, some 200 years after Riccioli.

So it looks as if this Italian priest was not just years ahead of his time; he was centuries ahead.

Amazing what you can find in these ancient texts.

Ref: arxiv.org/abs/1012.3642: The Coriolis Effect Apparently Described in Giovanni Battista Riccioli's Arguments Against the Motion of the Earth: An English Rendition of Almagestum Novum Part II, Book 9, Section 4, Chapter 21, Pages 425, 426-7

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