Wait a year. I’ll be cheaper.

by AlexWitherspoon
The $4400 Genome:
[Via ScienceNOW]

The cost of sequencing an entire human genome continues to plummet. Complete Genomics, a Mountain View, California-based biotechnology company last year claimed it would soon be able to sell full human genome sequences for as little as $5000 apiece. That now appears within reach. In tomorrow’s Science, the company will report that it sequenced three human genomes for about $4400 each, at least in the cost of reagents. Such cheap sequencing could vastly accelerate studies designed to pinpoint genes underlying complex diseases.
[More]

And they claim to be able to do it in a day! I’d like to see how accurate the data is but it does represent a huge decrease in time and money:

The rapid fall in sequencing prices may give genomics an equivalent of Moore’s Law, which describes how the number of transistors on computer chips doubles every 18 months, steadily driving down the cost of computing power. In 2003, the cost of sequencing a human genome was an estimated $300 million. That was down to $1 million in 2007 and $60,000 last year.

It is now dropping about an order of magnitude every 18 months or so. So by the end of next year, we could be looking at $500 genomes. As i said below, buy stock in hard drive makers.

Technorati Tags: Bioinformatics

Why networks are important

Starting a High Tech Business: No Cold Hires:
[Via Phil Windley's Technometria]

Image via Wikipedia

I’m starting a new business called Kynetx. As I go through some of the things I do, I’m planning to blog them. The whole series will be here. This is the twenty-first installment. You may find my efforts instructive. Or you may know a better way–if so, please let me know!

In the past two weeks Kynetx has doubled in size. There’s lots to do and the resources to make it happen, so getting more people became a priority. Getting the right people became the most important thing Steve and I could do for the long term health of the company.

I’ve been in lots of hiring situations before–at iMall we grew from three people to over 125 in a little over 16 months. I’ve learned a few things. The most important being that mistakes in hiring can cause untold grief later on down the road. You definitely want to get this right the first time–iterating to a solution is too expensive.

I’m in firm agreement with Joel Spolsky on what constitutes getting it right: hire people who are “smart and get things done”. That’s not easy; the good people aren’t usually out looking for jobs. They’ve already got jobs where they’re respected and well compensated because they’re “smart and get things done.”

One good rule of thumb for getting good employees is “no cold hires.” Four out of the five people we hired this past week are good friends who Steve and I have worked with in multiple ventures in the past. The fifth was someone who had worked closely with another key member of the team in mutliple ventures. We know these people well: we know their personality, we know their strengths, and we know their weaknesses. And…they know ours. Most importantly, we know they’re “smart and get things done.”

[More]

This is one reason why answering ads and sending out resumes are only a small part of looking for a job. They are necessary because they can work but sometimes only indirectly.

My first job, at Immunex, started as just a resume I sent to them. But it came across the desk of someone I had shared a room with at a recent conference. He knew me and instituted the interview process.

The resume was cold but the interview was hot.

That is why networking needs to be a constant and continuing process. Luckily, many people want to help you find a job. Humans are pretty nice that way. You just have to give them a way and networking is one way.

The hires may not be hot but lukewarm can make a big difference in this economic climate.

Technorati Tags: Economy, Government

Who are they empowering?

Microsoft erases the black guy:
[Via AMERICAblog: A great nation deserves the truth]

Notice any difference in these two pics from Microsoft’s USA and Poland Web sites?

USA:

Poland:

[More]

They kept the Asian dude but lost the Black guy. And they actually look like they obviously put a White guy’s head on top since the hands are still black!

What a bad Photoshop job. And let’s not even talk about the color scheme. MS marketing needs some real help.

Technorati Tags: General, Science, Technology

Weird Internet today

The internet has not been it reliable self recently. I was without Internet service on Friday due to a fire in a datacenter in downtown Seattle. Of course, trying to find out what was going on WITHOUT internet service was quite a chore.

I mean first I had to check my system, since the Verison modem was all green, indicating that it was connected fine. Everything checked out fine on my end.

I tried accessing Verizon via my iPhone. That worked but there was nothing at the Verizon site to explain the service outage, not even at the page called System Service.

So, after digging out an old bill, I found a number for the DSL service. After a fun phone tree, I got a recorded message that service in my area code was out and was expected back online in a few hours.

Which it was, saving me the worry of a July 4th weekend without internet.

Then today, accessing pages using several different browsers was really slow. Some sites would load fine (such as Amazon). Others would load very slowly or timeout before they were loaded. But email worked just fine. And my newsreader (NewsNetWire) was able to get the news feeds from sites that I could not get to directly from my browser!

I figured that perhaps email, using a different protocol, might be able to access the 4 different mail servers I use for different accounts but doesn’t the newsreader was using the same HTTP protocol that the browsers do. Well I’m self-educated so I might be missing something. (I tried playing around with changing DNS servers in case Verizon’s had been hosed but this did not help).

I was able to get Goggle News and see that there were a lot of government servers under a DDOS attack so I made the leap that that might be having some effect. Call it Internet magic.

So, with no real explanation, things have returned to normal. But I hate not knowing why.

Technorati Tags: Technology

Poll for Idea Club

We like to get the topics for the monthly Idea Club discussion from those attending or who are interested. We are currently polling for the topic that will be discussed on April 27. The choices are:

1. Green Microfinancing
2. Sustainable Urban Farming – like the White House is doing
3. Trucking of Tomorrow – how to transport the materials of the future between cities in a sustainable way
4. Moving Off the Grid – what technologies are available for either developed or developing world approaches
5. Getting Away from COFAs – Concentrated Animal Feeding Operations
6. Other – name your own topic

You can select as many topics as you’d like.

Technorati Tags: Sustainability, Web 2.0

Not good

by Joe Attardi
Every 30GB Zune In The World Froze At 2am This Morning [Microsoft]:
[Via Consumerist]

If you’re Steve Jobs, you probably dream of stories like this: Zunes all over the world foze up at around 2am this morning and won’t reboot, and nobody knows why.

ArsTechnica says it seems to have affected all owners of the 30 gig model, and hit no matter what you were doing at the moment:

[More]

This is an epic fail. Not only does something screw up, but it causes the player to crash and just became a brick. And all MS has said is:

Customers with 30gb Zune devices may experience issues when booting their Zune hardware. We’re aware of the problem and are working to correct it. The Zune Social might be slow or inaccessible. Sorry for the inconvenience, and thanks for your patience!

I figure to be zuned will appearon the Urban Dictionary soon.

Technorati Tags: General

Let’s vote on a slot machine

Greater Transparency for Slots Than Voting (Priorities Folks!):
[Via Concurring Opinions]

News from Underground has a priceless posting comparing the steps states take to ensure the accuracy and security of slot machines and e-voting machines. Here are some highlights. Nevada requires vendors of slot machines to provide it access to the machines’ software. By contrast, for most states, the source code for e-voting machines remains safely in the hands of vendors with no right of access provided to election officials or the public. A Nevada agency certifies slot machines, and the public has an opportunity to comment on that certification process. Depressingly, a select number of private companies certify e-voting machines at the vendor’s expense and the certification process is deemed a trade secret. Yes, even the certification process is hidden from public view.

The bottom line: the gaming business is subject to greater transparency and accountability than our voting process. It seems wrong, and a bit shameful, to associate a greater sense of responsibility and accuracy to gambling than voting. We care more about money earned through somewhat licentious means than our fundamental right to pick our elected officials in an accurate and secure manner. That seems to be where we are right now, but I have my hopes for the future. More to come on that in 2009. For now, happy holidays CoOp readers!

Maybe we should let the slot machine manufacturers produce out e-voting machines. Sounds like they could bring some valuable experience. I like the irony that the source code from the slot machines has to be open while the makers of voting machines are able to keep their code private for proprietary reasons.

Which one do you think is designed to make cheating more likely?

Technorati Tags: General, Politics

Fact-check

One of the things that Xconomy really seems to understand is the credo from Ken Layne “It’s the Internet and we can fact-check your ass.” The Web is a different medium and operates by different rles.

They do not seem to be afraid of interacting with a community in a fashion where their facts can all be checked. Most MSM are still afraid of their customers, viewing them as simply organisms whose purpose is to read ads and purchase from their advertisers.

The best info sites on the web realize that this is an interactive community. Xconomy shows signs of actually getting this and is rapidly becoming a must read for me. Also, while I already know Luke, I feel that I could walk up to Greg Huang or even even CEO Bob Buderi and begin a conversation. They are accessible in ways no MSM reporter is. I wonder if this helps them get leads for their stories?

Technorati Tags: General, Social media

Whither SGI?

by blakespot
Industry watching: Is this the end?:
[Via business|bytes|genes|molecules]

One wouldn’t have been able to tell looking at the huge Supercomputing booth, but SGI has been struggling for years. The company, whose machines were the mainstay of computational science, especially life science back in the day, and got this blogger through grad school, might just be on its final legs. Today, they received a delisting notice from the Nasdaq. Now, this is not the first time they’ve been in trouble, having filed for Chapter 11 in the past following delisting from the NYSE, so it’s entirely possible they will come out of it, but with the economy the way it is, and no real market for what they offer, I am not so sure. If it is the beginning of the end, it will be the end of a proud company that was once the epitome of visualization technology and built some of THE best computers ever made.

This is a shame. I go back to when Evans and Sutherland were the big computers used for visualizing all sorts of things. An old LDS-1 was the first ‘graphics’ computer I ever used, although the ‘pictures’ it showed were made up of many vector lines, not the smooth color-filled shapes we have today.

The Silicon Graphics came along, with its raster-based graphics and really fine looking representation of protein structure. While there was some competition with E&S systems, SGI was always the coolest. Great programs for representing biological structures and nice looking machines (colored plastics long before Apple). At one point in my career, I had a Mac as my regular computer and an old Indigo2 that the protein structure people gave me as a hand-me-down.

It was really sweet to have both computers working on structural problems at the same time.

Now it may be gone. E&S long ago left biological market, now making digital theaters and such.

Memories. E&S and SGI back when structural programs had great names like FRODO (I learned about this while at Rice from Jim Pflugrath who helped port it to an E&S PS300 while in Flo Quicho’s lab) and mice all had 3 buttons. #-D representations using blinking goggles synched to the monitor.

Now it can all be done by desktops. I do feel old.

Technorati Tags: Biology, Science, Technology

Great maps

Where Wars Kill People:
[Via Cosmic Variance]

The World’s Fair links to a great site at Telegraph.co.uk: the Atlas of the Real World. It’s a set of world maps (really cartograms), with the area of countries proportional to something more interesting than the mere land area – number of nuclear weapons, wealth in the year 1, and so on. Here is one to chew over: number of war deaths in the years since WWII.

Africa, the Middle East, and Asia. Latin America shows up just a bit. The big orange country in Asia is China, not Russia.

There are 18 maps and some of them are really interesting. NIce to have software that can help visualize data for us.

Technorati Tags: General

My first paid app

App Store Pick of the Week: Grocery IQ:
[Via Apple Hot News]

Thanks to Grocery iQ ($4.99), you may never have to write another shopping list. Now you can tap to quickly build a comprehensive and highly legible list on iPhone or iPod touch, arrange your list by aisle to match the layout of your grocery store, check off items as you add them to your cart, build a purchase history and a list of favorites. Grocery IQ even lets you email your list to a designated shopper.

Really nice execution.

Technorati Tags: General

Secret flash drive

Create a Secret Data Stash with a Fake Phonejack [Weekend Project]:
[Via Lifehacker]

While not as grandiose as having your own secret bookshelf door, constructing a hidden USB data stash won’t take a whole weekend and involve a table saw. At the DIY website Instructables there is a step by step tutorial on hiding your data behind a phone jack plate. By wiring a USB cord to the phone plate and making a USB cord with a phone jack terminal at one end, you’ll be able to access your secret data stash. If you’re not up for a bit of wire splicing and soldering, check out our top 10 USB thumb drive tricks.

Hidden USB Storage [Instructables]

This is very cool. Waiting to see it in a TV show soon.

Technorati Tags: General

A generational war

by kentbye
[Crossposted at SpreadingScience]
Social Media vs. Knowledge Management: A Generational War:
[Via Enterprise 2.0 Blog]

You’d think Knowledge Management (KM), that venerable IT-based social engineering discipline which came up with evocative phrases like “community of practice,” “expertise locater,” and “knowledge capture,” would be in the vanguard of the 2.0 revolution. You’d be wrong. Inside organizations and at industry fora today, every other conversation around social media (SM) and Enterprise 2.0 seems to turn into a thinly-veiled skirmish within an industry-wide KM-SM shadow war. I suppose I must be a little dense, because it took not one, not two, but three separate incidents before I realized there was a war on. Here’s what’s going on: KM and SM look very similar on the surface, but are actually radically different at multiple levels, both cultural and technical, and are locked in an undeclared cultural war for the soul of Enterprise 2.0. And the most hilarious part is that most of the combatants don’t even realize they are in a war. They think they are loosely-aligned and working towards the same ends, with some minor differences of emphasis. So let me tell you about this war and how it is shaping up. Hint: I have credible neutral “war correspondent” status because I was born in 1974.

[More]

A very clear post that describes the conflict between Boomer and Millennial thinking when it comes to dealing with large amounts of data. Knowledge management (Boomer) is a top-down put the data in the proper bin sort of approach. There are names for each bin and everything needs to fit in the correct one.

Social media (Millennial) uses human social networks in a bottom-up approach that allows the data to determine where it should go. Any bin that it should go into is an emergent property of the network created by the community.

Read the whole post for a nice dissection of what is happening in this War. Just remember that Age is not as important as attitude. There are Boomers who get social media and Millennials who do not.

I think it is that one personality wants things to be black and white (the data is in a database on THIS computer) white the other deals great with shades of gray (the data is in the cloud and not really anyplace).

I did my post-doc in a chemistry lab, the only biologist. I saw something very valuable. Chemistry is very process-driven. The purpose of a process is to reproduce success. If a process, say a particular chemical synthesis, did not work, as in the yield was 10% instead of 90%, it was not the fault of the process. The reagents were bad or the investigator was incompetent. But the process was still valid.

So chemistry selected for people who were very process-driven, wanted things very tightly controlled and well defined.

Biology has a very different regard for process. The same process (say the cloning of a gene) can be done on two different days and get different results (10 colonies of cells one day; 500 the next). Biology is really too complex to be able to control everything. A lot of things can go wrong and it can be really easy to fool oneself with results.

So biology, particularly at the cutting edge, selects for people who can filter out extraneous bits of data, can be comfortable with conditional results and with the general anarchy that can occur. Every molecular biologist has experienced the dreaded ‘everything stops working, so I have to remake every buffer, order new reagents and spend a month trying to figure out what happened, knowing that things will start working again for no real reason.’

Chemists in my post-doc lab hated biology because of the large variance in results, compared to chemistry. Biologists are often happy to be within an order of magnitude of expected results

One way of thinking has to know whether Schrodinger’s cat is dead or alive, while the other is comfortable with knowing it is simultaneously dead and alive.

Biology needs the Millenial approach because it is creating data at too fast a pace to put it all into bins. Social networks can help tremendously with the filters needed to find knowledge in the huge amount of data.

Technorati Tags: Science, Web 2.0

Helpful

Apple’s bid to change (browser) history:
[Via Buzzworthy]

Apple recently filed for a patent on a radically different way of organizing and navigating your browser history.
[More]

This could really be useful. A more graphically oriented view of history. But I wonder how you get a patent for something like this? Probably why I am not a patent attorney.

Technorati Tags: General, Technology

An interesting article

Overexpression of TOSO in CLL is triggered by B-cell receptor signaling and associated with progressive disease:
[Via BLOOD First Edition Papers]
Resistance towards apoptotic stimuli mediated by overexpression of antiapoptotic factors or extracellular survival signals like B-cell receptor stimulation (BCR) are considered to be responsible for accumulation of malignant B cells in CLL. TOSO was identified as overexpressed candidate gene in CLL applying unit-transformation assays of publicly available microarray datasets. Based on CLL samples from 106 patients, TOSO was identified to exhibit elevated relative expression of 6.8 compared to healthy donor B cells using quantitative real-time PCR (p=0.004). High levels of TOSO expression in CLL correlated with high leukocyte count, advanced Binet stage, previous need for chemotherapy and unmutated IgVH status. CD38+ CLL subsets harboring proliferative activity showed enhanced TOSO expression. We evaluated functional mechanisms of aberrant TOSO expression in CLL cells and identified TOSO expression significantly being induced by BCR stimulation compared to control cells (relative expression (RE) 8.25 vs. 4.86, p=0.01). In contrast, CD40L signaling significantly reduced TOSO expression (RE 2.60; p=0.01). In summary, we show that the anti-apoptotic factor TOSO is associated with progressive disease and enhanced in the proliferative CD38+ CLL subset. Both association with unmutated IgVH and the specific induction of TOSO via the BCR suggest autoreactive BCR signaling as a key mediator of apoptosis resistance in CLL.