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Life’s First Spark Re-Created in the Laboratory

Jun 28

Posted by Jeber in Musings

DNA Molecule display, Oxford University
Image by net_efekt via Flickr

A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn’t explain how these ingredients might have formed.

“It’s like molecular choreography, where the molecules choreograph their own behavior,” said organic chemist John Sutherland of the University of Manchester, co-author of a study in Nature Wednesday.

RNA is now found in living cells, where it carries information between genes and protein-manufacturing cellular components. Scientists think RNA existed early in Earth’s history, providing a necessary intermediate platform between pre-biotic chemicals and DNA, its double-stranded, more-stable descendant.

Like other would-be nucleotide synthesizers, Sutherland’s team included phosphate in their mix, but rather than adding it to sugars and nucleobases, they started with an array of even simpler molecules that were probably also in Earth’s primordial ooze.

They mixed the molecules in water, heated the solution, then allowed it to evaporate, leaving behind a residue of hybrid, half-sugar, half-nucleobase molecules. To this residue they again added water, heated it, allowed it evaporate, and then irradiated it.

At each stage of the cycle, the resulting molecules were more complex. At the final stage, Sutherland’s team added phosphate. “Remarkably, it transformed into the ribonucleotide!” said Sutherland.

According to Sutherland, these laboratory conditions resembled those of the life-originating “warm little pond” hypothesized by Charles Darwin if the pond “evaporated, got heated, and then it rained and the sun shone.”

Such conditions are plausible, and Szostak imagined the ongoing cycle of evaporation, heating and condensation providing “a kind of organic snow which could accumulate as a reservoir of material ready for the next step in RNA synthesis.”

Intriguingly, the precursor molecules used by Sutherland’s team have been identified in interstellar dust clouds and on meteorites. (Source-Wired)

It’s a fascinating development. We may not find a practical application of this information that’s acceptable to everyone any time soon, but just knowing that there is a reasonable explanation for the beginning of life is worthwhile.

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Physics discussion ends in skateboard attack

Jun 24

Posted by Jeber in Society

Sometimes we forget that once upon a time philosophers drank poison and submitted themselves to death at the stake, rather harsh criticisms of the philosophical arts. Then something like the following happens and we are once again reminded that philosophy can be dangerous. It seems contemplating physics is an especially risky occupation.

(06-24) 13:20 PDT SOUTH SAN FRANCISCO — A homeless man is on trial in San Mateo County on charges that he smacked a fellow transient in the face with a skateboard as the victim was engaged in a conversation about quantum physics, authorities said today.

Jason Everett Keller, 40, allegedly accosted another homeless man, Stephan Fava, on the 200 block of Grand Avenue in South San Francisco at about 1:45 p.m. March 30.evan

At the time, Fava was chatting with an acquaintance, who is also homeless, about “quantum physics and the splitting of atoms,” according to prosecutors.

Keller joined in the conversation and, for reasons unknown, got upset, authorities said. He picked up his skateboard and hit Fava in the face with it, splitting his lip, prosecutors said.

Fava also fell and broke his ankle, although how this happened wasn’t exactly known, authorities said.

The attack was witnessed by two other people who told police that Fava had done nothing to provoke Keller, authorities said.

Keller is expected to take the stand at his jury trial in the Redwood City courtroom of Superior Court Judge James Ellis.

E-mail Henry K. Lee at hlee@sfchronicle.com. (Source-sfgate.com)

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Facebook, thy name is vanity

Jun 12

Posted by Jeber in parody/satire

I can’t believe what a fuss people, well, tech people, ok, geeks, are making over the opportunity to reserve a vanity URL on Facebook tonight. There was a prolonged countdown hours before the window of opportunity opened, then a flood of postings showing off the URLs once obtained. It was near hysteria. People pushing and shoving, knocking the poor geeks glasses all askew. There might have even been a death or two from the crush of Facebookies trying to get through to the magic URL. The screaming of those poor souls being trampled, I’ll hear it in my mind for a long time. It may be muffled by all the other voices I hear in my head, but I’ll hear it, faintly, off in the background. facebook_1

I just can’t fathom such joy at such a dubious accomplishment. What does it say about the quality of your life when getting to have a personal URL on Facebook is the highlight of your week? How pathetic has your existence become when you feel proud to own a personalized URL on Facebook? What a complete loser you must be to feel compelled to announce to the world that you can now be found at facebook.com/ohlookatme/.

I’ll have more to say on this sad internet meme over on my Facebook page. That would be http://www.facebook.com/jack.carlson.

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Be honest; do you like me?

May 16

Posted by Jeber in Found Items, Humor

You worthless bag of filth

You vulgar little maggot.

You are a canker. A sore that won’t go away. I would rather kiss a slug than be seen with you. You’re a putrescent mass, a walking vomit. You are a spineless little worm deserving nothing but the profoundest contempt. You are a jerk, a cad, a weasel. Your life is a monument to stupidity. You are a stench, a revulsion, a big suck on a sour lemon.

You are a bleating foal, a curdled staggering mutant dwarf smeared richly with the effluvia and offal accompanying your alleged birth into this world. An insensate, blinking calf, meaningful to nobody, abandoned by the puke-drooling, giggling beast who sired you and then killed himself in recognition of what he had done. Your daddy was a bastard, your mamma was a whore, and you wouldn’t be here if the rubber hadn’t tore. I will never get over the embarrassment of belonging to the same species as you. You are a monster, an ogre, a malformity. I barf at the very thought of you.

You have all the appeal of a booger. Lepers avoid you. You are vile, worthless, less than nothing. You are a weed, a fungus, the dregs of this earth. And did I mention you smell?

You snail-skulled little rabbit. Would that a hawk pick you up, drive its beak into your brain, and upon finding it rancid set you loose to fly briefly before spattering the ocean rocks with the frothy pink shame of your ignoble blood.

May you choke on the queasy, convulsing nausea of your own trite, foolish beliefs. You are weary, stale, flat and unprofitable. You are grimy, squalid, nasty and profane. You are foul and disgusting. You’re a fool, an ignoramus. Monkeys look down on you. Sheep won’t have sex with you––only trash such as yourself.

You are unreservedly pathetic, starved for attention, and lost in a land that reality forgot.
And what meaning do you expect your delusionally self-important statements of unknowing, inexperienced opinion to have with us? What fantasy do you hold that you would believe that your tiny-fisted tantrums would have more weight than that of a leprous desert rat, spinning rabidly in a circle, waiting for the bite of the snake?

You are a waste of flesh. You have no rhythm. You are ridiculous and obnoxious. You are the moral equivalent of a leech. You are a living emptiness, a meaningless void. You are sour and senile. You are a disease, you puerile, one-handed, slack-jawed, drooling, meatslapper. On a good day you’re a half-wit. You remind me of drool.hobo

You are deficient in all that lends character. You have the personality of a used condom. You are dank and filthy. You are asinine and benighted. You are the source of all unpleasantness. You spread misery and sorrow wherever you go. You smarmy lagerlout git. You bloody woofter sod. Bugger off, pillock. You grotty wanking oik artless base-court apple-john. You clouted boggish foot-licking twit. You dankish clack-dish plonker. You gormless crook-pated tosser. You churlish boil-brained clotpole ponce. You cockered bum-bailey poofter. You craven dewberry pisshead cockup pratting naff. You gob-kissing gleeking flap-mouthed coxcomb. You dread-bolted fobbing beef-witted clapper-clawed flirt-gill.

You are a fiend and a coward, and you have toe jam. You are degenerate, noxious and depraved. I feel debased just for knowing you exist. I despise everything about you, and I wish you would go away forever.

I cannot believe how incredibly stupid you are. I mean rock-hard stupid. Dehydrated-rock-hard stupid. Stupid, so stupid it goes way beyond the stupid we know into a whole different dimension of stupid. You are trans-stupid stupid. Meta-stupid. Stupid collapsed on itself so far that even the neutrons have collapsed. Stupid gotten so dense that no intellect can escape. Singularity stupid. Blazing hot mid-day sun on Mercury stupid. You emit more stupid in one second than our entire galaxy emits in a year. Quasar stupid. Nothing in our universe can really be this stupid. Perhaps this is some primordial fragment from the original big bang of stupid. Some pure essence of a stupid so uncontaminated by anything else as to be beyond the laws of physics that we know. I’m sorry. I can’t go on. This is an epiphany of stupid for me.  (Source-though possibly not the original-Best of Craigslist)

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Happy Mother’s Day, Mom (1923-2007)

May 9

Posted by Jeber in Mother's Day

Dear Mom,

This marks the second Mother’s Day I’ve celebrated without you. As you knew full well, I’m not a believer in an afterlife, so I’m not deluding myself that you can actually read this from a higher plain or celestial viewpoint. But I see no reason I cannot address this to the you that lives on in my memory, the you I knew and loved for 53 years of my life, and continue to love to this day, your day, Mother’s Day.

Bertha Vivan Carlson (1923-2007)

Bertha Vivan Carlson (1923-2007)

You wouldn’t be surprised to learn that I have the same job and nearly the same daily routine I had when you were here. I have received a few pay raises, and it appears the store’s future is bright. Not much that happens every day is very different than it was back then. I’m still driving the same truck I’ve owned since 1998, the one you helped me buy by paying the down payment I couldn’t afford at the time. I still get home about the same time, still relax in front of the computer until bedtime, still have the TV on with a History Channel or Science Channel show playing in the background that I’m hardly paying attention to. I still spend most of my free time online, trying to help others in forums and learn more about technology from others in social networks. I still collect books like they were going out of style, reading them as often as possible. I still spend a few hours every week in my greatly reduced garden, tending the plants you and I both raised for years. Every one I transplanted from our old house to my current place has survived and flourished.

There have been a few changes since you left. I had to move out of the house we shared the last few years of your life, the one next door to the house you lived in for more than 20 years. I couldn’t afford a two bedroom house anymore. My current studio bungalow is about the right size for my needs. You’d feel right at home in my kitchen. Just about every dish, every pot and pan and every piece of cutlery I brought with me were once yours. Two years later and I still have those two boxes of brown sugar in my cabinet you bought and never used. I should throw them out but never seem to get around to doing it.

I also have a new companion, one I know you’d have loved as much as I do. Her name is Cleo, and she’s sleeping at my feet as I type this. Of all the animals I’ve owned and you met, she most closely resembles Bob the Malamute in attitude. She’s mellow, well behaved and easy going. Cleo is the perfect dog, a much better pup than I probably deserve to own. She goes to work with me every day and both the customers and my co-workers all love her. We just celebrated her 1st birthday last Friday at the store. I was tempted to rename her Bert to make up for having once named a pygmy goat after you. But she already knew her name when I adopted her, and I didn’t want to confuse her. Cleo doesn’t fit her as well as Bert would have, but there you go.

There isn’t much more news to catch you up on. I know you often said that your greatest satisfaction in life came from raising your two sons. In all honesty I can’t claim to have made as much of my life as your other son has, and as you well knew I made some dreadful mistakes that I have been able to outlive and to some extent make up for. You knew my good and bad points and were still always there for me.

I was fortunate to have you around for more of my life than many of my friends had with their mothers. You raised me well enough that I didn’t precede you in death or wind up in prison. Considering all I’ve done to make my own life inconsequential, it has instead turned out rather well. I give the credit for that to you and your influence. You were always patient, always supportive, always honest with me. It paid off.

You weren’t famous. You never made the national news. In your mind you were just a farm girl from Nebraska that moved to California after high school. You never were aware of your nearly unique status as a single working mother of two in the 1950s. You never took enough pride in the jobs you held until just shortly before your death. I don’t think you ever noticed how many lives you touched in a positive way, how many of your friends depended on your mid-Western practicality and no-bullshit way of expressing your ideas. You didn’t notice much of the influence you had on this world. But you did, and you still do.

Happy Mother’s Day, mom. I love you.

Jack

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Internet all a-Twitter

Apr 27

Posted by Jeber in Opinion, Twitter, web service

Poor Twitter.

Twitter gets raves when it proves to be useful and efficient but suffers predictions of its imminent demise when it’s used inappropriately. Reminds me of what Craigslist is going through. Read the headlines:

Swine flu creates controversy on Twitter

Some observers say Twitter — a micro-blogging site where users post 140-character messages — has become a hotbed of unnecessary hype and misinformation about the outbreak, which is thought to have claimed more than 100 lives in Mexico.

Swine Flu Misinformation Runs Rampant on Twitter

Still, mass hysteria and paranoia — with voices wailing over an ‘epidemic’ — continue to sweep the Net, especially Twitter.

It appears there’s confusion over the difference between a means of communication and the communications themselves.

Twitter is one medium among many that facilitate human communication. The internet is a free country, in a free country open communication is encouraged. While the methods used to communicate may differ in the degree of communications they permit, the means of communication do not dictate the substance of the communications. Twitter limits the conversation to less than 140 characters but it doesn’t guarantee the quality of the conversations one reads there. Perhaps there’s so much misinformation being spread around on Twitter because too many people are following those who spread it. If you walk too close behind the guy shoveling manure don’t complain when you get shit on your shoes.

Twitter has nothing to apologize for, has no reason to feel guilty or responsible for any hysteria about swine flu or any of the other thousands of inane and useless conversations going on at this very minute on its service.

There is a bit of a bright note to all this, though. The fact that the national media can casually toss off “Twitter” and “Craigslist” without feeling the need to go into much explanation shows just how common the knowledge of those two services has become to our society. It’s a sort of validation. They’ve joined the ranks of Google and AOL. There’s a difference, though. Increased awareness of Craigslist, eBay and Amazon means increased profits to someone, usually several someones. Increased awareness of Twitter doesn’t benefit anyone at the moment. In fact, increased awareness can also attract the lower lifeforms on the web. Spamming and spoofing are sure to increase on Twitter. The value of the experience will lessen for many users. “There goes the neighborhood” will be implied though not often explicitly stated.

Still, it would be nice if now and then the mass media and some bloggers would stop blaming the medium for the message.

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War, what is it good for?

Apr 6

Posted by Jeber in Musings&Mutterings, Society

Historically, wars were fought to increase the empire, conquor enemies, gain wealth and impose one society’s beliefs and customs on the rest of their (known) world. Two domestic benefits of warfare were employment for many of the young men and work for those who stayed home, manufacturing arms and munitions. war_production

In the 21st century we no longer occupy those lands we conquor, indeed we no longer even conquor our enemies to the same extent our ancestors did. We don’t kill every adult male or manchild, we don’t rape the women or take possession of all the livestock of our foe. We don’t even attempt to become benign overlords any more.

We do still send our young males, and now females, into harm’s way. We are on our way to making warfare more antiseptic and sterile, but we’re not there yet. We no longer reap the benefit of increased employment or manufacturing capabilities, since we can now use robotics to construct our instruments of war, requiring fewer humans and manufacturing plants. The battlefield will soon be overrun with robots. The new “frontlines” will be occupied by a person in the rear with a joystick and monitor. Our enemy’s tactics are changing, too. Our greatest enemies are foreign belief systems and computer viruses. Our nation’s freedoms have turned out to be a Trojan Horse.

War seems to be morphing into an activity that offers none of the rewards it traditionally has, none of the benefits. Soon it will become a completely senseless behavior. Yet humans are confrontational animals. Because we posses a sense of personal property we have also evolved attitudes and behaviors to provide for the defense of that property. When we perceive our nation as personal property (us vs. them) we extend that desire to defend our property to the national level. So it seems inevitable that mankind will continue to argue, assault and take up arms against neighbor and foreigner.

If conventional warfare no longer exists, how horrific is the future of human antagonism?

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Earth Hour-sending the wrong message?

Mar 28

Posted by Jeber in Ecology, Lights Out Day

I would like to think that any person living on this planet would have some concern for its well-being. It is, after all, the only home we have.

But too often good intentions are wasted on fadish events that provide a feel-good moment but produce no substantial benefits. I suspect the Earth Hour we’re all supposed to participate in tonight is one of those well-meant but ultimately pointless exercises.

Ariel Schwartz sums up my attitude nicely in an article written for Fast Company.

The logo for Earth Hour
Image via Wikipedia

Earth Hour is officially the kickoff for the WWF’s campaign to get world leaders to agree on a global deal at UN climate talks in December 2009, but it has morphed into much more than that. Turning out the lights for that one blessed hour is, according to WWF President and CEO Carter Roberts, “casting a vote in support of the future of the Earth.” Well, if that’s all we have to do to show that we’re in favor of sustainability, sign me up.

The truth is obviously more complicated than that, but there’s a real problem with Earth Hour: one hour of complete darkness is sending the wrong message to anyone who is not a staunch environmentalist. As George Marshall, the founder of the Climate Outreach Information Network, points out in the UK Guardian,  “Asking people to sit in the dark plays very well to a widely held prejudice that ‘the greens’ want us all to go back to living in caves.” Darkness symbolizes fear and negativity (ever seen a depressed teenager dress in all white?) while light symbolizes innovation, creativity, and everything else we love about civilization. There’s a reason that cartoonists put a lightbulb above characters’ heads when they come up with ideas.

Turning off the lights is poor symbolism. We need light, innovators, and creative people to get us through our energy crisis. Awareness isn’t always about cutting back. It’s also about moving forward. So today at 8:30 PM, I’m going to leave the lights on–at least until I leave the room.

It’s not that I refuse to acknowledge the impact human activity has had on our planet. It’s not that I don’t believe in conservation. I work for a company that embraces recycling and reuse. I preach that attitude frequently on our company website.

It’s just that I prefer expending our energy and social activism on efforts that produce sustainable results. I would rather endorse substantial changes in our society that result in a lasting improvement to our ecosphere. I think that Earth Hour fails to meet that criteria.

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Oh mighty ‘bama, where is thy transparency?

Mar 12

Posted by Jeber in Opinion, Politics

Politically and socially I’m moderate to liberal in my general outlook on life. I’m not so liberal as to have joined the Church of Saint Obama, though McCain was a poor alternative, I thought. Too much was being expected of Obama, and he didn’t do much to bring expectations back down to earth. He was aware of his cult status, his deification.

One of the promises made early and often by the president was transparency in government. That was perhaps the most dramatic and audacious guarantee he made us early on. After the last eight years many of us welcomed the idea of a more visible process. If we’re being asked to pay the bills, we ought to be able to know where the money’s going.

And Obama told us we would see his government working. He was going to make Washington a transparent town.

It appears he may have just broken that promise. How else are we to interpret the following but to conclude it’s business as usual, sadly.

How could this happen?

Barack Obama and Michelle Obama

Image via Wikipedia

We were asked to give him a pass on two aspects of his life. To support Obama was to willingly ignore the fact that he was a lawyer and a politician. He may have sounded refreshing, but the substance of Obama is deeply influenced by his love for the law on the federal level. He is a politician and a lawyer, just like Bush was a politician and a lawyer and like Nixon was a politician and a lawyer. Just like Lincoln was a politician and a lawyer.

I can only conclude that the following is an indication of that reality.

There are number of outstanding Freedom of Information Act (FOIA) requests for key documents, by groups like EFF, Public Knowledge, and KEI. In one of our FOIA requests, we asked for 7 specific documents, referenced by the exact title and date of the documents. These documents are the proposals for the text of the agreement.

The texts are available to the Japanese government. They are available to the 27 member states of the European Union. They are available to the governments of Canada, Mexico, New Zealand, Australia. They are available to Morocco, and many other countries. They are available to “cleared” advisers (mostly well connected lobbyists) for the pharmaceutical, software, entertainment and publishing industries. But they are a secret from you, the public.

Today we received this letter from the White House, Office of the United States Trade Representative. Our FOIA request was denied on the grounds that the documents are “information that is properly classified in the interest of national security pursuant to Executive Order 12958.”

Here is a link to a PDF of the denial of the FOIA request.  (Source: huffingtonpost.com)

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Diagramming the Beatles

Feb 26

Posted by Jeber in cartoons, fun, music

funny pictures
moar funny pictures

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Hello Twitter friends

Feb 11

Posted by Jeber in Twitter, on the web, social networking

This is one great group of people. You really should consider joining us on Twitter.

Get your twitter mosaic here.

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The Weekend Beat

Jan 24

Posted by Jeber in music, videos

Some unusual music to get your weekend started off with rhythm.

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Obama, day .5

Jan 20

Posted by Jeber in Opinion, Politics, in the news

It’s been a reality for half a day now, Obama is president. He wasn’t elevated to sainthood. He is not the chosen one of god to lead us into the promised land nor is he the anti-christ. He’s a guy. A smart (being learned is not a crime or sin), articulate, deliberate, former lawyer and educator, guy. We’ve also seen that he’s a professional politician. He knows how the game’s played. He’s no Jimmy Stewart, no Mr. Smith. But that’s not necessarily a bad thing. We expect a CEO to know how a company runs and what has to be done to accomplish the company’s goals.

At this point I’ll say he was a success if he just manages to keep things from getting any worse over the next 4 years. He cannot treat any problem before us as “business as usual”.

The economy isn’t just bad, we’ve seen how the system can be played and we will be far more hesitant to trust others with our money in the future. The weaknesses and potential for abuse of capitalism have been made clear. We are going to have to rebuild the economy while at the same time redesigning capitalism.

Not much different in foreign relations. We face an enemy both physical and economic. If we carelessly attempt to destroy terrorists at all costs, we risk not only destroying our economy but could destroy the country we’re trying to save. We need to not do the terrorist’s job for them.

Obama’s on a tightrope, and when you’re first learning to walk one, simply not falling off is a big accomplishment at the start.

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Cleo gets a makeover

Jan 3

Posted by Jeber in Cleo, pictures

In case it’s not clear, I should point out that Jeber’s is my personal blog. Here’s where I post any old thing I think of or come across on the ‘net that doesn’t fit into any of the topics that I blog about elsewhere. I have a tech blog and three with different takes on social issues. I even have a blog for my workplace. But Jeber’s is me, it relects perhaps most accurately my eclectic interests.

Lately I’ve been obsessing over my dog, Cleo. I apologize to you non-dog-lovers, but I’m just so blown away by her attitude, her innate good behavior and her silliness I just can’t stop talking about her. Thanks goodness my Flickr stream already had a lot of non-Cleo pictures in it or people would think I can only photograph a single dog.

In order not to highjack my own blog with picture after picture of Cleo, I’ve set up a separate page for my favorite shots of her. But that page is about to change.

I’ve found a cool new application called Jalbum. I’ll be using that to create a java page of all my favorite Cleo pics. It should be up shortly. I hope you enjoy viewing it as much as I had creating it.

(Note: I just learned one interesting tidbit about jalbum. Don’t try to share it with MySpace. It appears to be a violation of their TOS. Thankfully I was notified before I allowed it so I didn’t get my account closed.)

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Focused social networks-how many are too many?

Dec 30

Posted by Jeber in social networking

There can be no doubt, social networking is picking up steam.

When Facebook was still “thefacebook”, Harvard student Mark Zuckerberg intended it for use by his dorm mates. It quickly grew beyond Harvard and eventually accepted members from any college or university. It has continued to grow, and today anyone can join. Wikipedia lists their membership as of June, 2008, at 140,000,000.

MySpace opened its doors in 2003 as a service to eUniverse employees. Three years later it welcomed its 100 millionth member. This year membership is over 250 million.

Friendster, the grandaddy of social networking sites, began in 2002 as an invitation-only site. It’s growth hasn’t been as dramatic as Facebook and MySpace. Still it boasts over 90 million users today.

These sites all began as focused, localized networks of friends, fellows and co-workers. They quickly expanded into massive, open-to-all communities with members from nearly every nation on Earth. It appears that people on the internet, just like people in the real world, enjoy socializing with their friends and even strangers. Social networking has proven to be immensly popular, and it’s popularity continues. Wikipedia lists 132 networks active this year.

(image courtesy of mediaspin.com)

(image courtesy of mediaspin.com)

Now networking is once again returning to its roots. Businesses are incorporating social networking into the enterprise. Networking software is being developed to scale from a small business with few employees to global enterprises hosting several intranets. Even blogging platforms like Word Press are offering themes intended to act as social networks. Localized and focused are the new goals of many networks. Groups are forming among neighbors, students (deja vu all over again) and like-minded individuals with common social and philosophical interests.

Localized networks do have one weakness that doesn’t afflict the larger ones. Let’s say you’re a cat lover who wants to network with others who share your passion for kitties. Open your browser and Google for “social networks for cat lovers”. Of the 218,000 hits returned, let’s say that at least 10,000 of those are unique networks. How do you decide which one to join? They are all focused on cat lovers. Presumably all the members of those groups love cats. How will you select just one? What criteria can you apply to make your decision productive, and how will you apply that criteria? Maybe you can narrow down your choices to a group in your area, or one that is further focused on adopted cats, or Persians. Whatever means you use