Friday Cephalopod: “Dumbo” doesn’t do them justice [Pharyngula]

EVOLUTION IS BIOLOGICALLY IMPOSSIBLE

“Charles Darwin was daydreaming when he wrote that he could visualize “in some warm little pond,” with all sorts of salts and electricity, the spontaneous generation of the first living cell. Darwin’s dream of the magical powers of salts and electricity may have come from his grandfather. Mary Shelley wrote of him in 1831 in her introduction to Frankenstein. “They talked of the experiments of Dr. Darwin . . . who preserved a piece of vermicelli in a glass case, till by some extraordinary means it began to move with voluntary motion.” She goes on to speculate that galvanism (electricity) was the extraordinary means. All theories need testing, so I bought some vermicelli pasta, kept it in salt water in a test tube for a month, and never saw any motion, voluntary or otherwise. I also used a tesla coil to conduct “galvanism” through it to a fluorescent bulb. The bulb lit and the vermicelli eventually began to cook, but never came to life.

“Darwin’s bulldog,” Thomas Huxley, had a vision of himself on the early earth as “a witness of the evolution of living protoplasm from non-living matter.”In Huxley’s day, the cell was blissfully considered simply a blob of protoplasm. Huxley also may have read Mary Shelley’s subtitle to Frankenstein, “The Modern Prometheus.”Prometheus was the Greek mythical Titan, who formed a man of clay, then animated it. This myth may be the earliest reference to abiogenesis, the animation of inorganic materials. In order not to leave that possibility untried, I fashioned a clay man and directed the tesla-coil spark over it to light the bulb. The clay man was not animated.

Evolutionists currently invoke the “primeval soup” to expand the “warm little pond” into a larger venue, the oceans. They aim to spontaneously generate the first cell so they must thicken the salt water with (take a breath) polysaccharides, lipids, amino acids, alpha helixes, polypeptide chains, assembled quaternary protein subunits, and nucleotides, all poised to self-combine into functional cellular structures, energy systems, long-chain proteins and nucleic acids. Then during an electrical storm, just the right mix of DNA, mRNA, ribosomes, cell membranes and enzymes are envisioned in the right place at the right time and the first cell is thunderbolted together and springs to life. That marvelous first cell, the story goes, filled the oceans with progeny competing in incredible polysaccharide, lipid, amino acid, nucleotide, and cannibalistic feasts. The predators thereby thinned the soup to the watery oceans we have today while the prey escaped by mystically transmuting themselves into the current complex animals and plants, or perhaps vice versa because no one was there to record it. We are assured by the disciples of Darwin and Huxley that the “once upon a pond” story to obtain a blob of protoplasm is still sufficient for the spontaneous generation of the cell as we know it today. All demur when asked for evidence. All balk when asked to reverse-engineer a cell in the laboratory in spite of the fact that laboratories rival nature and reverse engineering is orders of magnitude easier than engineering an original design. One wonders why they balk if cell stuff is so easily self-generated and carbon molecules seem to have such an innate tendency to self-combine.

To test simply the alleged self-combining tendency of carbon, I placed one microliter of India (lampblack) ink in 27 ml. of distilled water. The ink streaked for the bottom of the test tube where it formed a dark haze which completely diffused to an even shade of gray in 14 hours. The carbon stayed diffused, not aggregated as when dropped on paper. At this simple level, there is no evidence that the “primeval soup” is anything but fanciful imagination.

In science, the burden of evidence is on the proposer of the theory. So although the evolutionists have the burden of providing evidence for their fanciful tales, they take no responsibility for a detailed account or for any evidence demonstrating feasibility. Contrarily, they go so far as to imply that anyone holding them to the normal requirements of science is feebleminded, deranged, or evil. For example, Professor Richard Dawkins has been quoted as saying, “It is absolutely safe to say that, if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid, or insane (or wicked, but I’d rather not consider that). “Instead of taking proper responsibility for the burden of evidence, the evolutionist propagandizes by the intimidation of name calling.

To set a better example, let us take up the evolutionist’s burden of evidence to see where it leads. Our first observation is that apparently all functions in a living organism are based largely upon the structures of its proteins. The trail of the first cell therefore leads us to the microbiological geometry of amino acids and a search for the probability of creating a protein by mindless chance as specified by evolution. Hubert Yockey published a monograph on the microbiology, information theory, and mathematics necessary to accomplish that feat. Accordingly, the probability of evolving one molecule of iso-1-cytochrome c, a small protein common in plants and animals, is an astounding one chance in 2.3 times ten billion vigintillion. The magnitude of this impossibility may be appreciated by realizing that ten billion vigintillion is one followed by 75 zeros. Or to put it in evolutionary terms, if a random mutation is provided every second from the alleged birth of the universe, then to date that protein molecule would be only 43% of the way to completion. Yockey concluded, “The origin of life by chance in a primeval soup is impossible in probability in the same way that a perpetual motion machine is impossible in probability.”

Richard Dawkins implicitly agreed with Yockey by stating, “Suppose we want to suggest, for instance, that life began when both DNA and its protein-based replication machinery spontaneously chanced to come into existence. We can allow ourselves the luxury of such an extravagant theory, provided that the odds against this coincidence occurring on a planet do not exceed 100 billion billion to one.”8The 100 billion billion is 1020. So Dawkins’ own criterion for impossible in probability, one chance in more than 1020, has been exceeded by 50 orders of magnitude for only one molecule of one small protein. Now that Professor Dawkins has joined the ranks of non-believers in evolution, politesse forbids inquiring whether he considers himself “ignorant, stupid, insane, or wicked.”

Let us proceed to criteria more stringent. For example, Borel stated that phenomena with very small probabilities do not occur. He settled arbitrarily on the probability of one chance in 1050 as that small probability. Again according to this more stringent criterion, we see that evolving one molecule of one protein would not occur by a wide margin, this time 25 orders of magnitude.

Let us go further. According to Dembski, Borel did not adequately distinguish those highly improbable events properly attributed to chance from those properly attributed to something else and Borel did not clarify what concrete numerical values correspond to small probabilities. So Dembski repaired those deficiencies and formulated a criterion so stringent that it jolts the mind. He estimated 1080 elementary particles in the universe and asked how many times per second an event could occur. He found 1045. He then calculated the number of seconds from the beginning of the universe to the present and for good measure multiplied by one billion for 1025 seconds in all. He thereby obtained 1080 x 1045 x 1025 = 10150 for his Law of Small Probability.

I have not been able to find a criterion more stringent than Dembski’s one chance in 10150. Anything as rare as that probability had absolutely no possibility of happening by chance at any time by any conceivable specifying agent by any conceivable process throughout all of cosmic history. And if the specified event is not a regularity, as the origin of life is not, and if it is not chance, as Dembski’s criterion and Yockey’s probability may prove it is not, then it must have happened by design, the only remaining possibility.

Now to return to the probability of evolving one molecule of one protein as one chance in 1075, we see that it does not satisfy Dembski’s criterion of one chance in 10150. The simultaneous availability of two molecules of one protein may satisfy the criterion, but they would be far from the necessary complement to create a living cell. For a minimal cell, 60,000 proteins of 100 different configurations would be needed.5,10 If these raw materials could be evolved at the same time, and if they were not more complex on average to evolve than the iso-1-cytochrome c molecule, and if these proteins were stacked at the cell’s construction site, then we may make a gross underestimation of what the chances would be to evolve that first cell. That probability is one chance in more than 104,478,296, a number that numbs the mind because it has 4,478,296 zeros. If we consider one chance in 10150 as the standard for impossible, then the evolution of the first cell is more than 104,478,146 times more impossible in probability than that standard.

Reproduction may be called a regularity because billions of people have witnessed billions of new individuals arising that way, and in no other way, for thousands of years. The origin of life was a unique event and certainly not a regularity. Therefore, according to mathematical logicians, the only possibilities left are that life either was generated by chance or by deliberate design. The standard for impossible events eliminated evolution so the only remaining possibility is that life was designed into existence. The probability of the correctness of this conclusion is the inverse of the probability that eliminated evolution, that is, 104,478,296 chances to one.

Although the certainty of design has been demonstrated beyond doubt, science cannot identify the designer. Given a designer with the intelligence to construct a cell and all life forms, it is not logical that he would construct only one cell and leave the rest to chance. The only logical possibility is that the designer would design and build the entire structure, the entire biosphere, to specified perfection. That seems to be as far as science can go.

Life was designed. It did not evolve. The certainty of these conclusions is 104,478,296 (1 followed by 4,478,296 zeros) to one. This evidence suggests a Designer who designed and built the entire biosphere and, for it to function, the entire universe. Primary and secondary sources from history properly provide additional information on the Designer because the biological sciences are not equal to that task.”

Joseph Mastropaolo, Ph.D. Physiology

Gadget Lab Podcast: Can I Use My iPhone’s NFC to Pay for My Uber?

WIRED

Now that we’ve got confirmation of an Apple announcement coming in less than two weeks (September 9 is the official date), it’s time to double down on the bets. What features are we going to see in the next iPhone? Both hosts are optimistic that we’ll see NFC and some sort of mobile payments architecture baked into the next Apple mobile—read Christina’s story about this if you haven’t already done so. All the other details, well, the guys are still a little murky on those. But that doesn’t stop them from speaking about them at length. Also, Mat and Mike discuss the latest developments in the war between Lyft and Uber. And Mat has some great ideas about how to earn a stack of one-star ratings when he starts his new career as a Lyft driver. You might want to stock up on lotions.

Listen to this week’s episode or subscribe in iTunes.

Send the hosts feedback on their personal Twitter feeds (Mat Honan is @mat, Michael Calore is @snackfight) or to the main hotline at @GadgetLab.

Game|Life Podcast: Nintendo Announcements, Nintendo Leaks

Shulk, the hero of Xenoblade Chronicles, as he appears in Smash Bros. for Wii U. Nintendo

Podcasts have a bit of a lead time, and sometimes things change between recording and release. In the case of this week’s Game|Life podcast, something that we discussed as a rumor—the hero of Xenoblade Chronicles appearing in Nintendo’s all-star fighting game Super Smash Bros.—came true this morning.

Additionally, although I mentioned on the podcast that we don’t yet have a price or release date for Nintendo’s Amiibo figurines, Nintendo has now announced… well, the price, anyway. ($12.99 each.)

But that’s cool! Join me, WIRED contributor Bo Moore and IT pro Josh Strom this week as we discuss these topics and things that did not get out from under us.

Game|Life’s podcast is posted on Fridays, is available on iTunes, can be downloaded directly and is embedded below.

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Flying a Blimp Is Way Trickier Than You’d Expect

Goodyear

Goodyear’s newest airship, just christened Wingfoot One, is now cruising the skies in all its newfangled glory. From the ground, the redesigned dirigible doesn’t look that different—it’s bigger, sure, but not much else. Not so from the cockpit. “From a pilot’s standpoint, it’s a night-and-day difference from the old model to the new airship that we’re flying,” says Goodyear pilot Derek Reid.

Pilots flying the old model operate a wheel and rudder system, like old-timey boat captains. The new model feels more like a videogame, with a joystick controlling pitch and yaw. A control panel displays electronic feedback from all flight control surfaces, and vectored engines can swivel in any direction, allowing the ship to take off and land like a helicopter and hover in place.

For all the innovation, though, the Wingfoot still moves on the relaxed timescale of an airship—it has a maximum speed of 73 miles per hour, compared to the old ship’s 50. “In order to be a good blimp pilot, you have to have patience—you aren’t going anywhere fast,” says Reid. “If you want to move fast, get in a Boeing 747.” (Typical cruising speed: 567 miles per hour.)

Despite those slow speeds, blimps are notoriously difficult to fly. (And with less than 40 blimp pilots in the world, it’s one of the rarest jobs on the planet.) There is no “flying by the numbers,” no set altitudes, airspeeds or power settings. The ship is so impacted by air pockets, wind and weather that a pilot needs to adapt moment-by-moment, operating by sense and intuition. “It’s seat-of-the pants flying,” says instructor pilot Mike Dougherty. “It’s different every time. No two take offs and landings are the same.”

Nor are any two airships the same. “Anyone that’s been around an airship will tell you that they have personalities,” says Reid, “little qualms that you have to get used to. Each one is different. It may sound like a superstition, but it’s really true.” Those who work around airships believe they take on the attitudes of their crews. Reid says he hasn’t figured out Wingfoot quite yet, but that it’s similar to its elders in at least one respect: “Even in a brand new ship like this, you still get that physical, romantic kind of flying that you don’t get in too many other aircraft.”

Switchboard Is Like Craigslist Without the Creeps and Flakes

Screenshot: WIRED

Most startups want to grow as fast as they can. For many in the tech game, including as Paul Graham, the founder Y Combinator, one of Silicon Valley’s hottest startup incubators, rapid growth is the very definition of a startup. So called “growth hackers” obsess over A/B testing and analytics, trying to maximize app downloads in an attempt to reach exponential expansion.

But not all tech companies see things this way. Take Switchboard. The Portland, Oregon-base outfit offers an online service that lets people create simple sites for online communities. Using a Switchboard site, you can either “ask” for something you need or “offer” something you have. That’s it. The larger Portland startup community uses it to post job listings, offer expertise, and announce hackathons. Oberlin College in Ohio uses it to help students and alums network with each other and share job opportunities. Then there’s The Meat Collective, which helps people buy and sell sustainably raised meat.

Mara Zepeda Ashley Forrette

The possibilities are limitless, but Switchboard has decided to grow slowly for now, limiting and carefully screening the creation of new communities. “We value the quality of the communities, not the quantity of communities,” says Mara Zepeda, the company’s co-founder and CEO. That may sound elitist, but it’s really about making sure that every user has a good experience, regardless of which Switchboard community they’re a part of. And that means taking time to make sure the service evolves in the right way.

Zepeda, a former journalist for National Public Radio, originally envisioned the service as a networking platform for her alma mater, Reed College in Portland, where she served on the alumni board. She took inspiration, oddly enough, from the U.S. Department of Agriculture’s Hay Net site, where farmers can either ask for hay or offer hay for sale. She and co-founder Sean Lerner built the original Switchboard just for Reed, but they quickly realized that the platform they’d built could be useful to other communities and decided to found a company.

Where the Money Is

Switchboard makes money in two ways. First, users can pay to promote particular posts. Second, organizations that collect money from members—such as Reed College, or nonprofit organizations—pay an annual fee for the Switchboard service. Other communities can use the service for free. It may seem therefore that it would be in the company’s best interest then to attract as many communities as possible. More communities would equal more users, and more users would equal more promoted posts—and therefore, more money. But Zepeda explains that Switchboard wants to avoid the site turning into a free-for-all for spammers, trolls and, well, jerks. To prevent this, the team is making sure that the early communities set the right tone for the future.

In general, they’re looking for people who are already at the center of a formal or informal community and want to find a better way to help its members connect with each other. One example is Wheelwomen, a community for women interested in cycling, founded by Elly Blue, who previously founded a community called Portland Society, for professional women in Portland with an passion for bikes. Wheel Women members use the site to buy and sell bikes, swap information about great bike trails, find places to stay with other members while traveling, and—this seems to be Switchboard’s favorite activity—post job opportunities.

There are thousands of different tools for building interactive websites, ranging from Facebook groups to private web forum software. But Blue says Switchboard is perfect for the Wheelwomen community. The structure is limited, but that’s a strength, she says. It helps keep things simple and focused. “It kind of keeps the internet trolls in all of us at bay,” she says.

And the focus on quality seems to be working. Although Switchboard includes tools to flag spam or inappropriate comments, Blue says no one has flagged anything on the Wheelwomen Switchboard yet, nor has she had to delete any posts. It has also helped foster a sense of intimacy and trust. “All of the people who will respond to you are part of a community,” she says. “You might not know them but you might not know them but you probably know someone who knows them.”

The Sense of Trust

This sense of trust is a big part of the reason Switchboard isn’t trying to grow too quickly. But it has made fundraising difficult. Switchboard was rejected by Y Combinator, and most Valley-based venture capitalists have shrugged off the company. But Zepeda thinks, ultimately, this was a good thing. “I’m so glad Y Combinator rejected us,” she said in a speech at the TechFestNW conference in Portland earlier this month. When Y Combinator president Sam Altman asked Zepeda to re-apply, she and Lerner declined, deciding to stick to their Portland roots and focus on slow growth. “We were being asked to move to a monoculture,” she said at the event. “We were being asked to move to a factory farm.”

The big question, though, is whether this sort of slow growth will make it harder to actually make money. But she thinks the slow and steady route will help build a more sustainable business in the long run. And she’s not alone. Zepeda sees Switchboard as part of a growing community of companies she calls “feeders.”

These range from other tech companies like Caterina Fake’s Findery to restaurants and food trucks. These businesses are, in many ways, the exact opposite of a Silicon Valley startup. They’re not trying to “disrupt” anyone, just build sustainable businesses that help other people. They tend to be founded by women, immigrants, veterans, the disabled, and other people who are left behind by the modern tech industry. “That’s because they know what scarcity looks like,” she says. “And they have an incredible ability to transform it into abundance. That sounds like a pretty good business model to me.”

And all of these companies have a healthy understanding of food, whether that’s through a corporate culture that values cooking for each other, as at Switchboard, or by actually feeding people, like a catering business. She cites Soylent—the Y Combinator backed company that makes meal replacement shakes—as the antithesis of a feeder company. “This company was built by people who are the opposite of providers,” she says. “To them, nourishment isn’t a gift but a chore. This is the opposite of a feeder mentality.”

With New 3DS Model, Nintendo Continues Pursuing Hardcore Gamers

Nintendo’s New 3DS, announced today, has a number of upgrades aimed at hardcore gamers. Nintendo

Nintendo’s got a brand new 3DS, one that’s aimed at capturing more of the hardcore gamer market.

Announced today for an October 11 release in Japan, the New Nintendo 3DS (that’s its name) has a variety of upgrades that all seem to be aimed squarely at gamers that demand high-end experiences. It now has a second analog joystick, making camera controls in complex games like Monster Hunter significantly easier. Going along with that are two extra “shoulder buttons” on the back of the unit for more control options. The 3-D screen and camera have been given upgrades.

And most significantly, New Nintendo 3DS has more under the hood. The internals have been upgraded for flashier graphics and faster internet speeds. Nintendo being Nintendo, it hasn’t said how much of a boost New 3DS will get. But it has said that the new model will actually play some exclusive games that wouldn’t be possible on the current 3DS.

The smaller version of New Nintendo 3DS. Nintendo

The first of these will be Xenoblade Chronicles, a version of the role-playing game that Nintendo released a few years back on its original Wii console. This is about as nerdy and hardcore-focused a piece of content as one could imagine: Nintendo launching a new platform with a 40-hour RPG? Who’d have imagined this in the days of Wii Sports?

Nintendo will release the New Nintendo 3DS in two models, roughly equivalent in size to the original 3DS and to the scaled-up 3DS XL model. They will retail for 18,800 yen and 16,000 yen respectively (about $180 and $160).

Other new features on both models include built-in support for near-field communication devices like Nintendo’s upcoming Amiibo interactive figures, more battery life and Micro SD card support.

Retreating Upmarket

Nintendo’s announcement of an upgraded portable machine designed to appeal to more discriminating, dedicated gamers comes hot on the heels of new comments by the company’s game design guru Shigeru Miyamoto that seemed to signal just this sort of shift.

Nintendo, he said to Edge magazine, no longer wants to chase after “the sort of people who, for example, might want to watch a movie. They might want to go to Disneyland.”

“Their attitude is, ‘okay, I am the customer. You are supposed to entertain me,’” Miyamoto said according to the report. “It’s kind of a passive attitude they’re taking, and to me it’s kind of a pathetic thing. They do not know how interesting it is if you move one step further and try to challenge yourself [with more advanced games].”

“Abandoning the lower-performance segments of an industry and moving upmarket is 100% predictable in disruption theory,” game design consultant Ben Cousins wrote on Twitter this week in response. “Was Miyamoto saying casual gamers were pathetic when the Nintendo stock was at $76?”

Advocates of disruption theory in books like The Innovator’s Dilemma—that’s one of the biz-school tomes that Nintendo name-checked when it launched the revolutionary Wii and DS hardware—would say that Nintendo is “retreating upmarket.”

Losing the “expanded audience” that it once courted to great effect with simplified gaming platforms—whether to mobile phone games or Disneyland—Nintendo is now, at least in the short term, pursuing the high-end consumer with products more geared to their needs. That’s more buttons, more joystick, more RPGs and more oomph.

You might notice that this is not a good long-term strategy, and indeed might be setting Nintendo up for death by a thousand cuts. That’s why Nintendo’s also working on its Quality of Life health-related gaming platform initiative, which might actually be able to capture a brand new audience again.

‘Til then, it’s “What, you want buttons? Here’s all the buttons.”

Oh, dear [Pharyngula]

The context of this graph isn’t entirely clear, but it’s from Jeffrey Ross-Ibarra of UC Davis, and it’s from a poll of 800 first year students, so I presume it’s the results of a survey of their incoming class?

Maybe one of the things we need to do as part of popularizing science to the general public is to emphasize the diversity of life, and talk more about the cool things plants and bacteria and fungi and so forth do. I know I started out as a zoologist, am still mostly focused on animal development, but over the years I’ve become increasingly aware that there are amazing contrasts to be studied. We might wish we could study aliens from Mars, but every time I look at plant development, for instance, I feel like I’m examining extraterrestrials already.

This Is How You Have to Ship Bugatti’s $3M Supercar

Spencer Berke/Symbolic Motors San Diego

When you drop $3 million on a special-edition Bugatti Veyron Grand Sport Vitesse, you want everything to be perfect. That’s why, before it leaves the factory, Bugatti wraps the car more carefully than royal nurses swaddle the future King George.

This Vitesse, complete with a custom (and questionable) paint job, was delivered to an unnamed buyer at Symbolic Motor Car Company in San Diego. Spencer Berke, an employee at the dealership, photographed the whole unloading process, which took more than two hours from start to finish.

Nearly the entire car is carefully wrapped for protection against scratches, with holes left open for ventilation at the front and exhaust at the rear, and a more translucent covering over the windshield. Only the driver’s door is left uncovered, so the car can be driven on and off a truck during shipping. Each spoke on the rims is individually wrapped with cloth and zip ties. A special mount to store the car’s removable hard top in a garage is included in a separate box. The cars, built in Molsheim, in eastern France, are generally shipped by boat, but impatient customers can have them air mailed for an extra fee.

With 1,200 horsepower, a top-speed of 255 mph, and a 0-60 time of less than 2.6 seconds, the Veyron Grand Sport Vitesse is fantastic machine, and Bugatti and its dealers do everything they can to keep it that way en route from the factory to the owner’s garage.

Once it’s unwrapped, the dealership spends up to 12 hours inspecting every detail, down to the finish, battery, fluids, and wiring. “If you’re going to ship a $3 million car, you want to make sure that it arrives intact and in a presentable condition,” says Rick Ahumada, sales manager at Symbolic. “Every car is special ordered to the client’s requests and tastes. It’s what you would expect of a $3 million car.”

How to Use OS X Yosemite’s Best New Messages Features

Screenshot: WIRED

Apple’s latest desktop operating system, OS X Yosemite, won’t officially come out until sometime this fall. But now that its public beta is open, both developers and a large number of Mac owners are able to use a preview version of the landmark OS.

For those who’ve just started using the beta, or are just anticipating its launch later this year, we’ve got some tips on how to best take advantage of the redesigned OS and its many new features. In this edition, we take on the new features in Messages. Messages spans both iOS 8 and Yosemite, but we’ll focus on the OS X side.

Messages has some great new features, especially for group chats, which historically have tended to get out of hand. In the upper right of a chat you get a new Details button. You can tap that to give a particular conversation a title, mute notifications for the chat, add participants, or remove yourself from the thread entirely. If everyone uses iOS 8 and Find My Friends, you can also share your locations with each other. Your positions are tacked onto a map. This Details button also houses a reverse chronological collection of the photos sent in the messaging thread, like a dedicated private photo stream for a conversation.

Through this details panel you also have the option to select a specific contact in the conversation to voice call, FaceTime, or share your screen with. When you make a request to share your screen, you can accept, decline, or block a user. A screensharing icon shows up in the upper menu bar of your homescreen which you can tap for additional controls like enabling or disabling audio chatting, pausing or ending the screenshare, or allowing the other person to control your screen. This should be incredibly useful for troubleshooting family iOS or OS X issues.

In the shift from making voice calls to more often texting with friends and family members, I occasionally lament being able to hear their voice—but not so much that I’d want to go back and forth leaving voicemails. Those days are definitely over. But that’s where a new feature called Soundbites come in. This is something other messaging apps like WhatsApp have offered for a while, and while you could always choose to send an audio file over text on iOS, this built-in functionality makes it far quicker and simpler.

Soundbites makes it possible to send audio messages to a friend which they can open and listen to at their leisure, without the urgency of a phone call. On the Mac, and in iOS 8, you tap a microphone button to the side of the message compose field to record one of these audio clips to send over Messages. The message is sent as a blue Message bubble the recipient can tap to download and play, and both you and the recipient can individually choose to keep it, or let it expire into the ether of ephemeral, self-destructing messages after a two-minute time span. In the beta I’m using, the audio is noisy and compressed sounding, more like it’s coming from a CB radio rather than a desktop computer, but I’d expect this quality to improve over time. Also in its current implementation, soundbites exist solely within a messaging thread, they aren’t collected in the Details panel for easy perusal later. It could be handy to have these voice messages collected in a single place, but we’ll see if that’s something Apple decides to change as the product evolves.

The beta of Messages works quite well, and the changes Apple has made to the experience, while some are quite subtle, are all positive improvements should you choose to use them. For me, now that I can mute chatty conversation threads, I think I’ll be using Messages far more on the desktop than I did before.

Home is where the microbes are

A person's home is their castle, and they populate it with their own subjects: millions and millions of bacteria.

A study published tomorrow in Science provides a detailed analysis of the microbes that live in houses and apartments. The study was conducted by researchers from the U.S. Department of Energy's Argonne National Laboratory and the University of Chicago.

The results shed light on the complicated interaction between humans and the microbes that live on and around us. Mounting evidence suggests that these microscopic, teeming communities play a role in human health and disease treatment and transmission.

"We know that certain bacteria can make it easier for mice to put on weight, for example, and that others influence brain development in young mice," said Argonne microbiologist Jack Gilbert, who led the study. "We want to know where these bacteria come from, and as people spend more and more time indoors, we wanted to map out the microbes that live in our homes and the likelihood that they will settle on us.

"They are essential for us to understand our health in the 21^st century," he said.

The Home Microbiome Project followed seven families, which included eighteen people, three dogs and one cat, over the course of six weeks. The participants in the study swabbed their hands, feet and noses daily to collect a sample of the microbial populations living in and on them. They also sampled surfaces in the house, including doorknobs, light switches, floors and countertops.

Then the samples came to Argonne, where researchers performed DNA analysis to characterize the different species of microbes in each sample.

"We wanted to know how much people affected the microbial community on a house's surfaces and on each other," Gilbert said.

They found that people substantially affected the microbial communities in a house -- when three of the families moved, it took less than a day for the new house to look just like the old one, microbially speaking.

Regular physical contact between individuals also mattered -- in one home where two of the three occupants were in a relationship with one another, the couple shared many more microbes. Married couples and their young children also shared most of their microbial community.

Within a household, hands were the most likely to have similar microbes, while noses showed more individual variation.

Adding pets changed the makeup as well, Gilbert said -- they found more plant and soil bacteria in houses with indoor-outdoor dogs or cats.

In at least one case, the researchers tracked a potentially pathogenic strain of bacteria called Enterobacter, which first appeared on one person's hands, then the kitchen counter, and then another person's hands.

"This doesn't mean that the countertop was definitely the mode of transmission between the two humans, but it's certainly a smoking gun," Gilbert said.

"It's also quite possible that we are routinely exposed to harmful bacteria -- living on us and in our environment -- but it only causes disease when our immune systems are otherwise disrupted."

Home microbiome studies also could potentially serve as a forensic tool, Gilbert said. Given an unidentified sample from a floor in this study, he said, "we could easily predict which family it came from."

The research also suggests that when a person (and their microbes) leaves a house, the microbial community shifts noticeably in a matter of days.

"You could theoretically predict whether a person has lived in this location, and how recently, with very good accuracy," he said.

Researchers used Argonne's Magellan cloud computing system to analyze the data; additional support came from the University of Chicago Research Computing Center.

The study was funded by the Alfred P. Sloan Foundation. Additional funding also came from the National Institutes of Health, the Environmental Protection Agency, and the National Science Foundation.

Other Argonne researchers on the study included Argonne computational biologist Peter Larsen, postdoctoral researchers Daniel Smith, Kim Handley, and Nicole Scott, and contractors Sarah Owens and Jarrad Hampton-Marcell. University of Chicago graduate students Sean Gibbons and Simon Lax contributed to the paper, as well as collaborators from Washington University in St. Louis and the University of Colorado at Boulder.

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Small molecule acts as on-off switch for nature's antibiotic factory: Tells Streptomyces to either veg out or get busy

Scientists have identified the developmental on-off switch for Streptomyces, a group of soil microbes that produce more than two-thirds of the world's naturally derived antibiotic medicines.

Their hope now would be to see whether it is possible to manipulate this switch to make nature's antibiotic factory more efficient.

The study, appearing August 28 in Cell, found that a unique interaction between a small molecule called cyclic-di-GMP and a larger protein called BldD ultimately controls whether a bacterium spends its time in a vegetative state or gets busy making antibiotics.

Researchers found that the small molecule assembles into a sort of molecular glue, connecting two copies of BldD as a cohesive unit that can regulate development in the Gram-positive bacteria Streptomyces.

"For decades, scientists have been wondering what flips the developmental switch in Streptomyces to turn off normal growth and to begin the unusual process of multicellular differentiation in which it generates antibiotics," said Maria A. Schumacher, Ph.D., an associate professor of biochemistry at the Duke University School of Medicine. "Now we not only know that cyclic-di-GMP is responsible, but we also know exactly how it interacts with the protein BldD to activate its function."

Streptomyces has a complex life cycle with two distinct phases: the dividing, vegetative phase and a distinct phase in which the bacteria form a network of thread-like filaments to chew up organic debris and churn out antibiotics and other metabolites. At the end of this second phase, the bacteria form filamentous branches that extend into the air to create spiraling towers of spores.

In 1998 researchers discovered a gene that kept cultured Streptomyces bacteria from creating these spiraling towers of fuzz on their surface. They found that this gene, which they named BldD to reflect this "bald" appearance, also affected the production of antibiotics.

Subsequent studies have shown that BldD is a special protein called a transcription factor, a type of master regulator that binds DNA and turns on or off more than a hundred genes to control biological processes like sporulation. But in more than a decade of investigation, no one had been able to identify the brains behind the operation, the molecule that ultimately controls this master regulator in Streptomyces.

Then scientists at the John Innes Centre in the United Kingdom -- where much of the research on Streptomyces began -- discovered that the small molecule cyclic-di-GMP is generated by several transcription factors regulated by BldD. The researchers did a quick test to see if this small molecule would itself bind BldD, and were amazed to find that it did. They contacted longtime collaborators Schumacher and Richard G. Brennan Ph.D. at Duke to see if they could take a closer look at this important interaction.

The Duke team used a tool known as x-ray crystallography to create an atomic-level three-dimensional structure of the BldD-(cyclic-di-GMP) complex.

BldD normally exists as a single molecule or monomer, but when it is time to bind DNA and suppress sporulation, it teams up with another copy of itself to do the job. The 3D structure built by the researchers revealed that these two copies of BldD never physically touch, and instead are stuck together by four copies of cyclic-di-GMP.

"We have looked through the protein databank and scoured our memories, but this finding appears to be unique," said Brennan, who is a professor and chair of biochemistry at Duke University School of Medicine. "We have never seen a type of structure before where two monomers become a functional dimer, with no direct interaction between them except a kind of small-molecule glue."

To confirm their findings, Schumacher determined several crystal structures from different flavors of bacteria (S. venezuelae and S. coelicolor) and came up with the same unusual result every time.

Now that the researchers know how cyclic-di-GMP and BldD can become glued together to turn off sporulation and turn on antibiotic production, they would like to know how the complex can become unglued again to flip the switch the other way.

The research was supported by a Long Term EMBO Fellowship (ALTF 693-2012), a Leopoldina Postdoctoral Fellowship, the Biotechnology and Biological Sciences Research Council (BB/H006125/1), the MET Institute Strategic Programme, and the Duke University School of Medicine.

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The above story is based on materials provided by Duke University . Note: Materials may be edited for content and length.

Up to 3,000 times the bacterial growth on hollow-head toothbrushes

Solid-head power toothbrushes retain less bacteria compared to hollow-head toothbrushes, according to researchers at The University of Texas Health Science Center at Houston (UTHealth) School of Dentistry.

The results of the study are published in the August issue of the Journal of Dental Hygiene. Lead author and professor at the UTHealth School of Dentistry, Donna Warren Morris, R.D.H., M.Ed., notes that microbial counts were lower in the solid-head toothbrush group than in the two hollow-head toothbrush groups in 9 out of 10 comparisons.

"Toothbrushes can transmit microorganisms that cause disease and infections. A solid-head design allows for less growth of bacteria and bristles should be soft and made of nylon," Morris said. "It is also important to disinfect and to let your toothbrush dry between uses. Some power toothbrushes now include an ultraviolet system or you can soak the head in mouthwash for 20 minutes."

The study was conducted over a three-week period where participants brushed twice daily with one out of three randomly assigned power toothbrushes. Participants used non-antimicrobial toothpaste and continued their flossing routine throughout the study, but refrained from using other dental products like mouthwash.

"The packaging on most power toothbrushes won't distinguish between a hollow-head and a solid-head design," Morris said. "The best way to identify a solid-head design is through the connection to the body of the power toothbrush. Naturally, there will be some space to connect the two parts but a significant portion will be solid, up to the bristles or brush head."

During the study the brush heads were exposed to five categories of oral microorganisms: anaerobes and facultative microorganisms, yeast and mold, oral streptococci and oral enterococci anaerobes, Porphyromonas gingivalis and Fusobacterium species.

The article also states that there is no present or published study that has demonstrated that bacterial growth on toothbrushes can lead to systematic health effects, but as Morris stated, several microorganisms have been associated with systemic diseases.

"We do know and there are studies that have linked Fusobacterium to colorectal cancer. Some of these other bacteria have been linked with cardiovascular disease," Morris said. "There is a high association with gum disease and cardiovascular disease. Researchers have been able to culture the same bacteria around the heart that causes gum disease. "

This study was funded in part by the Advanced Response Corporation. Other researchers include Millicent Goldschmidt, Ph.D., M.S., professor emerita at the UTHealth School of Dentistry; Harris Keene, D.D.S., retired professor from The University of Texas M.D. Anderson Cancer Center; and Stanley Cron, M.S.P.H., research instructor at the UTHealth School of Nursing.

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The above story is based on materials provided by University of Texas Health Science Center at Houston . Note: Materials may be edited for content and length.

Synthesis produces new fungus-derived antibiotic

A fortuitous collaboration at Rice University has led to the total synthesis of a recently discovered natural antibiotic. The laboratory recreation of a fungus-derived antibiotic, viridicatumtoxin B, may someday help bolster the fight against bacteria that evolve resistance to treatments in hospitals and clinics around the world.

As part of the process, Rice organic chemist K.C. Nicolaou and structural biologist Yousif Shamoo and their colleagues created and tested a number of variants of viridicatumtoxin B that could lead to the simplified synthesis of a new generation of more effective antibiotics.

The work reported this month in the Journal of the American Chemical Society (JACS) focused on a tetracycline discovered in 2008 by scientists who isolated small amounts from penicillium fungi. The yield wasn't nearly enough for extensive testing, but it provided a basis for the discoverers to analyze its structure through magnetic resonance imaging, Nicolaou said.

"We're inspired by molecules that are biologically active and have the potential to become medicines one day," he said.

The new discovery belongs to a class of antibiotics known as tetracyclines for their distinctive molecular structure. They proved potent in initial tests on Gram-positive bacteria, so named for a staining technique to mark bacteria that are more susceptible to antibiotics than their Gram-negative counterparts.

The first tetracyclines, discovered in the late 1940s, ushered in a new class of powerful antibacterial agents to treat high-mortality diseases, among them anthrax and plague as well as such bacterial infections as chlamydia, syphilis and Lyme disease.

To find new weapons, especially against "superbugs" that resist nearly all antibiotics, synthetic chemists pursue the complex process of mimicking the structures of effective natural molecules as they build drug candidates atom by atom.

"Tetracyclines are widespread antibiotics today, but bacteria are building resistance to a lot of them," Nicolaou said. "This new tetracycline is not plentiful in nature, so the only way we can make it available to study by biologists for its potential in medicine is to synthesize it in the laboratory."

Three years of effort led the chemists working at Rice's BioScience Research Collaborative to find a structure that not only matches that of natural viridicatumtoxin B, but also allows the possibility of synthetic variants that could match or surpass its antibiotic potency.

Nicolaou, who is best known for synthesizing the widely used anticancer drug taxol and the chemotherapy agent calicheamicin, said the complicated new molecule offered a challenge he couldn't resist. "The structure (the discoverers) assigned to this molecule was suspicious to us. We didn't actually believe that it was correct," he said.

"Given this, we initiated a research program to synthesize this compound for three purposes," he said. "One was to develop new synthetic chemistry, which is always the case in these kinds of endeavors. Two was to synthesize the molecule itself and confirm its structure. Three was to use the technology we've developed to make analogs of it in the hope that we could find something simpler and yet better in terms of its biological and pharmacological properties."

Nicolaou's team met all of those goals and did indeed revise the structure of the molecule. The lab turned synthetic samples over to biologist Shamoo and his group for testing against a number of bacterial strains and comparison with natural viridicatumtoxin B.

"This was very exciting for us," said Nicolaou, who moved his lab from the Scripps Research Institute and the University of California at San Diego last year to form these kinds of collaborations. "In order to investigate the biological properties of our synthesized compounds, we turned to the Shamoo laboratory for its expertise in the area of antibiotics and drug-resistant bacteria."

The biologists reported that the synthetic version performed as well as the natural, and analogs lacking a hydroxyl group were even more effective against the same Gram-positive bacteria. The results also suggested the possibility of making variants by modifying certain domains of the molecule to improve its overall pharmacological properties.

"The most important finding was that simpler variations that are easier to make are showing equal if not better activity than the natural substance," Nicolaou said.

"My lab was really excited about working with K.C.'s group," Shamoo said. "Our expertise in antibiotic resistance and his synthesis of viridicatumtoxin B and analogs were a perfect opportunity for us to work together on an important problem."

Nicolaou acknowledged it could be years -- even decades -- before an antibiotic derived from viridicatumtoxin B is available to patients. But, he said, careful research from the start pays dividends in the long term, and the tools developed through the process should prove valuable in the synthesis of other fungal tetracyclines.

"Even though you find something that looks good, you shouldn't take the first substance from the shelf and run to develop it into a drug," he said. "We have to worry about solubility, biodegradation, availability and so many different things before we can get on the path of clinical development, because that part of the process is very expensive. We want to be sure at the research stage that we're doing everything we can to ensure the success of our chosen drug candidate."

The subject is very much on his mind these days. In this month's print edition of the journal Angewandte Chemie, Nicolaou laid out strategies for drug development to make what he called "one of the most challenging and difficult human endeavors" more efficient.

"It's said that for a drug to be discovered, a chemist has to make 10,000 compounds on average," he said. "It also means that it takes 12 to 15 years to develop a drug from the beginning to the end, and costs between $1.5 billion to $2 billion.

"Often, these things are not predictable, so experimentation is usually the final proof of what we're trying to do. That's what makes our collaborations at Rice so welcome and fruitful. The interface between chemistry and biology is the key to success in discovering drugs."

Co-authors of the JACS paper are graduate students Christopher Hale, Lizanne Nilewski and Kathryn Beabout and postdoctoral fellows Christian Nilewski, Heraklidia Ioannidou and Abdelatif El Marrouni, all of Rice, and Tim Wang, a Rice undergraduate student and Rice Century Scholar. Hale, Ioannidou, El Marrouni and Christian and Lizanne Nilewski came to Rice from the Scripps Research Institute, where they initiated the project in Nicolaou's lab; Lizanne Nilewski is now a second-year graduate student in the lab of Rice Professor James Tour. Shamoo is Rice's vice provost for research and a professor of biochemistry and cell biology. Nicolaou is the Harry C. and Olga K. Wiess Professor of Chemistry.