Mark Twain used to toss around a saying about three kinds of lies. There are lies, damned lies, and statistics. This week in biotech, we saw some statistics that could lead some people to get a false impression that everything is just peachy in biotechland.

If you measure the state of life science innovation by the amount of money flowing in, things look swell. Venture capitalists poured $4.73 billion into 446 biotech companies last year, according to the MoneyTree report by the National Venture Capital Association and PricewaterhouseCoopers, based on data from Thomson Reuters. The venture industry association’s press release cheerily noted that overall venture funding jumped 22 percent last year. While software is still the No. 1 and faster-growing sector of the two, biotech held its own, with a solid 22 percent gain in dollars invested compared with a year earlier.

You have to dig deeper to see what’s really going on. There is still a good amount of money going toward late-stage development of drugs people started working on 10-15 years ago. But there is an alarming drop in support for today’s cutting-edge biotech startups. Last year, just 153 U.S. biotech and medical device startups got their first round of financing, the lowest amount of seed investment activity in 15 years, as reported by Ryan Flinn of Bloomberg News.

There’s something really wrong with this picture. Most any biologist will tell you we are living in a golden age of discovery, at a time when we will soon be sequencing entire human genomes for $1,000 in one day. We are able to ask questions about how life works that nobody could even imagine asking a few years ago. It ought to be the time to charge ahead with basic research, and early-stage R&D to test exciting new concepts in diseases like cancer, diabetes, Alzheimer’s, HIV, and more.

But everywhere you look, the story is about cuts, cuts, cuts. The National Institutes of Health, the primary government agency that supports basic biomedical research, used to write checks for one out of every three grant applications, but it’s now down to about one out of every six, NIH director Francis Collins said earlier this month at the JP Morgan Healthcare Conference. Pharma companies are cutting back on R&D, firing workers left and right, and leaning on cheaper outsourced vendors everywhere they can. As many as one-fourth to one-half of biotech venture capitalists are thought to be slowly going out of business, as they are unable to raise new investment funds. The same IPO investors that want to buy Facebook shares look at biotech stocks like a four-year-old looks at lima beans.

There are good reasons why we see all those things happening. Pharma companies have created enormous inefficiencies for themselves through mega-mergers, and now they need to spend years trying to get their houses in order. Biotech as an industry has overpromised and underdelivered, and many investors are tired of it. The FDA, stung by various drug safety scandals, has been cautious about approving new drugs (although there are signs that FDA leadership wants a more balanced approach). And of course, our society is still struggling to come to terms with healthcare reform, and the realization that it’s unsustainable to spend infinite amounts of money on healthcare.

John LaMattina

All that said, an entrepreneur or a bold Big Pharma executive is the kind of person who looks at that picture and believes he or she can overcome the hurdles, and form a plan to turn vision into reality. But there aren’t that many people out there with the can-do spirit, or guts, to put down real money behind really talented teams devoted to the discovery of new drugs. And because everybody’s talking about how to go from Phase I to Phase II with drugs people invented years ago, there’s a real possibility that once those projects run their course, we’ll all look around in 2020 and wonder where all the wonderful new drugs are going to come from.

“You can really get into a vicious cycle when you have to eat your own seed corn,” says John LaMattina, a senior partner with PureTech Ventures, and the former president of R&D at Pfizer.

There are exceptions, of course, with a few people trying creative new ways to plant seed corn. Third Rock Ventures and Atlas Venture are a couple of VC firms that have remained active, continuing to bet big on the edgiest stuff coming out of the labs. Most every Big Pharma company has set aside cash for corporate venture firms that are seeking to help fill the void being created by the shrinkage of traditional VC. Pfizer, Johnson & Johnson, Sanofi, Bayer, and deserve credit for working on creative new collaborations with top biomedical universities and research centers, which seek to minimize some of the problems with the fruitless alliances of the past. J&J made news this past week when it unveiled an incubator for 18-20 startups in San Diego which looks to fill up some lab space it had vacated through its own internal R&D cutbacks.

Right now, we are in an age of experimentation with new organizational structures for supporting biomedical R&D. The hope is that these new organizations can reduce the time, money, and high-risk profile that has made life sciences such a hit-or-miss investment over the years. Pharma companies know they don’t … Next Page »

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Yesterday, we ran the first half of the Seattle life sciences year in review, which focused on biopharmaceutical companies and global health organizations. Today’s rundown will cover the medical device, diagnostic, and health IT side of the local life sciences cluster.

Medical devices may not fare so well in a glamour contest, but this year the Seattle device community had more success stories, more acquisitions, upheaval, and even a couple of controversies. SonoSite was the biggest acquisition of the year, and although terms weren’t disclosed, it was almost surely followed by Pacific Bioscience Laboratories (the maker of the Clarisonic skin brush you see prominently displayed at Nordstrom). Calistoga Pharmaceuticals, you had a great year, but your deal is probably the third-biggest of the year in Seattle biotech. Sorry.

For the highlights from Seattle med-tech, diagnostics, and various Bio-IT operations, read on:

Sonosite (NASDAQ: SONO): The maker of portable ultrasound machines has been relatively stable, and modestly profitable as an independent company for some time, so I was surprised to see it get acquired for $995 million earlier this month by Japan-based Fujifilm. Shareholders can’t complain, given the price represents a 50 percent premium over SonoSite’s prior closing stock price. This is the biggest deal of the year in local life science, by a long shot.

NanoString Technologies. This was a big year for NanoString. The company, a spinoff from the Institute for Systems Biology, developed a second-generation version of its digital nCounter instrument, which measures the extent to which multiple genes are turned on or off in a biological sample. This was part of a bold plan to turn this scientific instrument into a diagnostic tool. By the end of the year, NanoString had raised another $20 million from GE, former Genzyme CEO Henri Termeer, and others, and it presented some important data that suggests it could compete with Redwood City, CA-based Genomic Health (NASDAQ: GHDX) in the breast cancer diagnostic market.

Clarisonic. Terms weren’t disclosed, but this could be the second-biggest acquisition of the year in Seattle’s life sciences community (although this company is hard to really categorize). Pacific Bioscience Labs, the maker of the Clarisonic skin brush, was acquired by cosmetics giant L’Oreal last month. The Clarisonic surpassed the $100 million sales mark in 2010, was highly profitable, and growing by leaps and bounds. My best guess is that Clarisonic sold for about $500 million. It’s the second home run for the same entrepreneurial team who developed the Sonicare toothbrush.

Geospiza. The Seattle-based developer of software … Next Page »

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We here at Xconomy are eagerly anticipating our biggest Seattle biotech event of the year: “The Immunex Impact.” We expect to pack the house tomorrow night at the Institute for Systems Biology in Seattle, as more than 230 people have registered. There is still a little bit more room to squeeze a few more folks in, but not much.

For those who may have missed the earlier announcements, this event will bring together many of the key people who built the Seattle biotech cluster through their experience at Immunex and other companies. We’re going to do our best to conjure up old memories about the spirit that made Immunex so special during its 20-year run in business.

Here’s what to expect. During the networking portion of the evening, before and after the program, we’ll be playing the 2002 soundtrack from the Immunex house band, 51 You. My favorite track on this CD has to be “Don’t Fear the Merger,” a clever play on Blue Oyster Cult’s “Don’t Fear the Reaper.”

Also during the networking, we’re putting together an awesome display of memorabilia. We will have old photos, T-shirts, a lab coat, trophies, coffee mugs, annual reports, back copies of the “Immunews” newsletters, a banner, and all kinds of other Immunex goodies to display. A certain co-founder (that’s you, Steve Gillis) says he’s willing to poke around in his basement to look for a copy of the “Wayne’s World” video spoof on some certain uptight East Coast pharma executives. I’m counting on you to deliver, Gillis!

But seriously, I want to thank Janis Wignall, Stewart Parker, Jake Johnston, my former Seattle Times boss Rami Grunbaum, and Stewart Lyman for contributing to this awesome stash of company memorabilia.

Once the clock strikes 6 pm, Leroy Hood, the president of the Institute for Systems Biology, will start off the program with some brief welcoming remarks as the host. Maybe he can enlighten us all about how in the early ’80s he got involved in co-founding Amgen (but not Immunex).

After I go through the usual round of thank-yous, the program will feature several well-known veterans of Immunex. I’ll moderate a keynote chat between co-founders Steve Gillis and Chris Henney, which will go for about 20 minutes. Then we’ll hand over the microphone to a group of Immunoids who will each tell a single favorite anecdote from their experience back in the day. Doug Williams, Stewart Parker, Janis Wignall, Steve Graham, Dave Urdal, and Patricia Beckmann will each have their turn to share a fond memory.

Lastly, I’ll wrap up by offering a special mystery prize to the winner of the Immunex trivia quiz, which I published here on Xconomy a couple weeks ago. The bar has been set pretty high, but there’s still time to send in your answers to me at ltimmerman@xconomy.com.

That’s it. We plan to wrap up the program by 6:45 pm, so that all the Immunoids and friends can connect over a drink and some light fare. See you there at the Institute for Systems Biology tomorrow night.

Here’s the agenda:

5 pm: Registration/Networking

6 pm: Welcoming remarks: Leroy Hood

6:05 pm: Introductions: Luke Timmerman

6:10 pm: Keynote chat with Steve Gillis and Chris Henney

6:30 pm: Remembrances

Doug Williams, Biogen Idec

Stewart Parker, IDRI

Steve Graham, Fenwick & West

Janis Wignall, consultant

Dave Urdal, Dendreon

Patricia Beckmann, OTRADI

6:45 pm: Trivia quiz winner announced

6:45 pm-8:30 pm: Networking

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Patricia Beckmann has covered lots of bases in biotech—science, venture capital, entrepreneurship, and state officialdom. But once an Immunoid, always an Immunoid. So I’m excited to have her join Xconomy as one of the speakers at our next big Seattle life sciences event, “The Immunex Impact,” on Dec. 1.

For those who may have lost track, Beckmann is now the executive director of the Oregon Translational Research and Drug Development Institute (OTRADI) in Portland. Like the name suggests, its goal is to help researchers in Oregon translate their biological ideas into valuable new medical products. You can read more about Beckmann’s career and the Oregon initiative in this Science profile from earlier this year.

Beckmann’s enduring claim to fame comes from her scientific contributions at Immunex to the blockbuster autoimmune disease drug etanercept (Enbrel). That product, first approved in 1998, is on track to be the world’s third-best selling drug with $8 billion in worldwide sales in 2014, according to Thomson Reuters. But Beckmann has done a lot of interesting things since then. She managed life sciences investments for Paul Allen’s Vulcan for a while in the 2000s, followed by a stint at the Seattle-based Accelerator. There, she was the founding chief scientist of Homestead Clinical, a Leroy Hood project that was shut down for a while but has since been reborn as Integrated Diagnostics.

We have a great lineup of Immunex vets who have agreed to tell a short story about one of their best memories from their Immunex days. We’ll start things off with a keynote chat between co-founders Steve Gillis and Chris Henney, and then Beckmann will join Stewart Parker, Dave Urdal, Janis Wignall, Steve Graham, and Doug Williams in the “short stories” part of the program.

Patricia Beckmann

Beckmann admits to having once received the fabled “Pons and Fleischmann” award for dubious achievement in science, and she hinted that she might have something to say about that during the event. The award was just one symbol of Immunex’s famously irreverent scientific culture, which encouraged people to try risky things that might fail in the lab. Pons and Fleischmann inspired the award after they were celebrated for discovering cold fusion in the 1980s, at least until other scientists learned that wasn’t really true.

Anyway, this event will be held from 6 pm to 8:30 pm on Dec. 1 at the Institute for Systems Biology’s new headquarters in Seattle’s South Lake Union neighborhood. Tickets have been going fast, and it’s possible at this rate that it will sell out a week or two in advance. So get your tickets now, and get ready for a fun evening of networking and reminiscing with the people who built Seattle’s signature biotech company, and who are continuing to make things happen in the Northwest life sciences community. See you there Dec. 1.

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Immunoids, and friends of Immunoids, listen up. Come December, it will be 10 years since Immunex agreed to be acquired by Amgen. I figure it’s the perfect time to reunite the people who lived through the exhilarating, and sometimes terrifying, experience of building Seattle’s first major biotech company.

So I’m super-psyched to say that we are bringing together a dream team of Immunex alumni for Xconomy’s next big event in Seattle, called “The Immunex Impact” on December 1.

Here are the confirmed speakers who will be there to tell a few war stories from their Immunex days, and to connect with lots of friends old and new:

—Steve Gillis, Immunex co-founder, now managing director, Arch Venture Partners

—Christopher Henney, Immunex co-founder, now chairman and interim CEO, Oncothyreon

—Doug Williams, Immunex chief technology officer, now executive vice president of R&D, Biogen Idec

—Stewart Parker, Immunex’s first employee, now CEO, Infectious Disease Research Institute

—Steve Graham, Immunex’s longtime corporate attorney, now co-chair of life sciences, Fenwick & West

—Janis Wignall, Immunex scientist and science education leader, now a consultant

—Dave Urdal, Immunex president of manufacturing, now chief scientific officer, Dendreon

I plan to make sure the speeches are short and sweet, leaving plenty of time for what this event is really about. It’s a chance to connect and re-connect with the Immunex network that continues to make a big impact on Seattle biotech every day.

Steve Gillis

This event will be from 6 pm to 8:30 pm on December 1 at the Institute for Systems Biology’s new headquarters in South Lake Union. ISB president Lee Hood (not a co-founder of Immunex, but a biotech industry godfather nonetheless) is planning to provide some opening remarks. I’m going to encourage him to reminisce a bit about what he was doing in 1981 when this whole biotech business started really taking off.

As if you couldn’t already tell, I’m chomping at the bit to get this event started. To get your tickets, check out the new “Immunex Impact” registration page here. See you there at the ISB on December 1.

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Alan Aderem, the immunologist who co-founded the Institute for Systems Biology a decade ago with Leroy Hood and Reudi Aebersold, is leaving the Seattle research center to take over the presidency of another of one of the Northwest’s other leading centers of biomedicine—the Seattle Biomedical Research Institute.

Aderem, 55, is joining Seattle BioMed as director, and taking a team of more than 40 people from the Institute for Systems Biology with him to carry out research into new vaccines and drugs for global health. By January 1st, Aderem will step up the ladder as president of Seattle BioMed, replacing founder and president Ken Stuart in the top decision-making role. Stuart, 70, will remain on the Seattle BioMed faculty, and on the board of trustees. A $7 million grant from the Bill & Melinda Gates Foundation is helping bring the people, technology and equipment over to Seattle BioMed.

The leadership switch represents a major shift in the Seattle research community. Aderem has long been seen as the logical successor at the ISB to Hood, the biotech pioneer who turned 72 last fall. Besides giving Aderem a chance to move up, the switch represents a philosophical evolution for global health, by intensifying its emphasis on the “systems biology” approach—which seeks to analyze entire biological systems in concert instead of one gene, one protein, one pathogen, at a time.

“When Lee and Reudi and I co-founded the ISB 10 years ago, my idea was always to apply the new field to global health,” Aderem says. “I was director for most of the time I was there. Now, the time has come, and the field of systems biology has significantly matured, so I can focus on what I want to focus on, which is global health. This is the right place.”

Stuart, who founded Seattle BioMed back in 1976, said he’s “looking for another hand on the helm.” He will go back to his primary passion, working in the lab, while continuing to work on board-level issues and fundraising for the institute.

The actual move of scientists from the ISB is coming in a couple of phases, and will start the first week of April, Stuart says. Once it’s complete, Seattle BioMed will have grown into an organization with about 375 employees, and an annual budget of about $60 million—a 20 percent increase over where it is today, Stuart says. Aderem has teams who work on influenza, tuberculosis, HIV, and basic immunology—all of whom are making the move to Seattle BioMed, he says. The associate director of the Institute for Systems Biology, John Aitchison, is also joining Seattle BioMed, while maintaining an affiliation with the Institute for Systems Biology, Aderem says.

Ken Stuart (left) and Alan Aderem

While all of Aderem’s grant support will follow him to Seattle BioMed—which means both dollars and people will flow away from the Institute for Systems Biology—Aderem said he and Aitchison still plan to collaborate with their former colleagues. Hood was supportive of the move, Aderem says. The two remain “close personal friends,” Aderem says, adding, “when I started thinking about this, Lee was one of my confidantes. We talked a lot about it. As time went on, he understood my passion for it, and was quite supportive. Lee is a great optimist.”

Hood, when I spoke to him briefly this afternoon, said he expects a couple new faculty members to join his Institute later this year, which will “roughly” replace the people who are departing for Seattle BioMed. He said the move by Aderem is a sign of the maturation of systems biology—but that personal factors were involved in the decision, too.

“Alan has wanted to assume a leadership role for some time, and I’m not ready to step down,” Hood says. “This is a logical place for him to go. It was a matter of … Next Page »

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[Updated: 3:35 pm] Thanks to everyone who joined us yesterday for the latest Xconomy Seattle event, “Computing in the Age of the $1,000 Genome.” We packed the room once again for a highly engaging conversation about the state of the art in genomics. We dug into both the technical and cultural barriers that need to come down before this edgy science will come close to living up to its promise for personalized medicine.

We had a terrific group of speakers yesterday to engage with a sharp audience that kept them on their toes. The speakers included Leroy Hood of the Institute for Systems Biology, Bob Nelsen of Arch Venture Partners, Complete Genomics CEO Cliff Reid, PacBio chief scientist Eric Schadt, Rowan Chapman of Mohr Davidow Ventures, Rob Arnold of Geospiza, Ilya Kupershmidt of NextBio, Deepak Singh of Amazon, Jim Karkanias of Microsoft, Paul Rutherford of EMC/Isilon, and Tim Hunkapiller, a consultant with Life Technologies.

Special thanks go out to Swedish Medical Center for graciously opening up its Pinard Auditorium on the Cherry Hill Campus. Thanks also to yesterday’s event sponsors—the Institute for Systems Biology and Complete Genomics. And thanks to Isilon for handing out a nice little goodie for attendees—100 hardcover copies of Kevin Davies’ new book “The $1,000 Genome: The Revolution in DNA Sequencing and the New Era of Personalized Medicine.” They were all snapped up by the time I left.

One other thing I was happy to see yesterday is that more and more biotechies are getting serious about exchanging ideas on Twitter. We had some pretty lively accounts firing around Twitter yesterday, which were compiled under the hash tag #1kgenome.

Those following the Twitter stream found out fast that a certain Microsoft exec suggested to Lee Hood that Seattle needs an SGI, sort of like BGI (the emerging powerhouse known as Beijing Genomics Institute). Here are the folks I know who were Tweeting during the proceedings. I’m probably forgetting somebody, so if you were there and Tweeting, let me know at ltimmerman@xconomy.com and I’ll add you to the list.

Adriana Alejandro @alalejandro

Sally James @jamesian

Todd Smith @finchtalk

Sandra Porter @digitalbio

Richard Gayle @rbgayle

Tobin Arthur @tjarthur

Jon Izant @sagebio

Melissa Tizon @melissatizon

Jonathan Sheffi @sheffi

Deepak Singh @mndoci

Christophe Trefois @trefex [Added: 3:35 pm]

Taking notes, I’ve found, is pretty hard to do while you’re emcee of an event, but taking photos is another story. So I pulled out my camera and snapped a few images (which you can click on directly to enlarge). We’re just getting warmed up with a pretty ambitious event schedule for 2011, so stay tuned to this space for future updates on the next Xconomy event we have in store.

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What will your doctor be able to tell you when your entire genome can be sequenced in an afternoon for $1,000 or less? Who out there in the business world has a handle on how to make this data useful? Will it actually help our society improve health and wellness?

I’m getting my game face on for a sold-out event we’re hosting this afternoon in Seattle called “Computing in the Age of the $1,000 Genome.” Registration for this half-day forum starts at around 1:15 pm, and the program will get going at 2 pm. As usual at Xconomy events, we’ll have networking before and after we hear from our all-star cast of speakers. The event will be at Swedish Medical Center’s Cherry Hill campus, Pinard Auditorium, 550 17th Avenue in Seattle.

Here’s a reminder of who’s coming to join the conversation. See you over there.

Leroy Hood, the co-founder and president of the Institute for Systems Biology, Seattle

Cliff Reid, co-founder and CEO, Mountain View, CA-based Complete Genomics

Eric Schadt, chief scientific officer, Menlo Park, CA-based Pacific Biosciences

Jim Karkanias, senior director, applied research and technology, Microsoft Health Solutions, Redmond, WA

Deepak Singh, senior business development manager, Amazon Web Services, Seattle

Rowan Chapman, partner, Menlo Park, CA-based Mohr Davidow Ventures

Andreas Sundquist, co-founder and CEO, Palo Alto, CA-based DNANexus

Ilya Kupershmidt, co-founder and VP of products, Cupertino, CA-based NextBio

Rob Arnold, president, Seattle-based Geospiza

Tim Hunkapiller, Seattle-based consultant, Life Technologies

Paul Rutherford, chief technology officer, Isilon Storage Division, EMC, Seattle

Bob Nelsen, managing director, Arch Venture Partners, Seattle

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We all have 3 billion chemical units of DNA in each of our cells, and scientists say they will soon be able to unravel our unique genome sequences for $1,000 or less. Since genes get dialed up or down at different points in life, when we are healthy or diseased, scientists want to sequence our genomes many times to track changes through life.

But in an ocean of data this immense, how in the world will computer scientists find what’s really important to an individual’s health? How will the Northwest’s big infotech companies help scientists store, analyze, visualize this bewildering amount of data? When will the average patient start to see benefits from the long-promised era of personalized medicine?

I’m getting ready to ask questions like those, and more, at Xconomy Seattle’s next big event “Computing in the Age of the $1,000 Genome.” This gathering will be on Monday afternoon, February 7, at Swedish Medical Center’s Cherry Hill campus. I’ve put together a program designed to maximize interaction between the speakers and the audience. That means there will be time for Q&A, and no time for PowerPoint.

The event will start with a fireside chat I will moderate between a couple fierce competitors in the faster/cheaper sequencing world—Cliff Reid, the CEO of Mountain View, CA-based Complete Genomics (NASDAQ: GNOM) and Eric Schadt, the chief scientific officer of Menlo Park, CA-based Pacific Biosciences (NASDAQ: PACB). Then we’ll have a panel discussion with three entrepreneurs with different takes on computational biology, moderated by a venture capitalist with a lot of experience in the field—Rowan Chapman of Mohr Davidow Ventures.

Following a networking break, we’ll re-convene with a panel that brings together key people at Northwest tech giants that all have ideas on how to profit from the opportunity in gene sequencing. Deepak Singh of Amazon Web Services, Jim Karkanias of Microsoft Health Solutions, and Paul Rutherford of EMC’s Isilon Storage Division will talk about how they see this landscape evolving in a panel moderated by Tim Hunkapiller, a Seattle-based consultant with Life Technologies, who was recently called a “Pillar of Genomics” by GenomeWeb.

Then we’ll close things out with what it sure to be a lively fireside chat. I’ll moderate a conversation with Leroy Hood of the Institute for Systems Biology and Bob Nelsen of Arch Venture Partners. Hood, as many Seattleites know well, has spent the past few years describing his vision for “P4 Medicine.” Nelsen—someone who’s unafraid to speak his mind in public—will offer his thoughts on where this field is heading. He’s been watching this phenomenon for years, as his firm has invested in the market leader in faster/cheaper gene sequencing, San Diego-based Illumina (NASDAQ: ILMN) and the Icelandic genetic research operation deCode Genetics.

Only a few tickets remain for this special event, so it’s best to reserve a seat now rather than try to get one at the door. We will have a couple other special features at this event, including an educational exhibit from the folks at the Northwest Association for Biomedical Research, which should be fun and interesting. See you there on Monday.

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If scientists will soon be decoding entire human genomes in an afternoon, for $1,000 or less, how will that change the way we think about health and wellness? What are the business opportunities for companies that figure this out early? How will tech companies handle the gargantuan IT challenges of separating signal from the noise in the billions of genomic data points on each of us?

Can you tell I’m starting to get fired up about Xconomy Seattle’s next big event, “Computing in the Age of the $1,000 Genome?” We are less than two weeks away from this rare assembly of West Coast infotech and biotech talent, which will be held the afternoon of February 7th at the Pinard Auditorium at Swedish Medical Center’s Cherry Hill Campus. A few tickets are left for this gathering, but it is on track to sell out in advance. Even though the speakers are primarily from Seattle and San Francisco, we have had a few prominent attendees say they are flying in from around the country for this gathering.

As a reminder, here’s the lineup of speakers.

—Leroy Hood, the co-founder and president of the Institute for Systems Biology, Seattle

—Cliff Reid, co-founder and CEO, Mountain View, CA-based Complete Genomics

—Eric Schadt, chief scientific officer, Menlo Park, CA-based Pacific Biosciences

—Jim Karkanias, senior director, applied research and technology, Microsoft Health Solutions, Redmond, WA

—Deepak Singh, senior business development manager, Amazon Web Services, Seattle

—Rowan Chapman, partner, Menlo Park, CA-based Mohr Davidow Ventures

—Andreas Sundquist, co-founder and CEO, Palo Alto, CA-based DNANexus

—Ilya Kupershmidt, co-founder and VP of products, Cupertino, CA-based NextBio

—Rob Arnold, president, Seattle-based Geospiza

—Tim Hunkapiller, Seattle-based consultant, Life Technologies

—Paul Rutherford, chief technology officer, Isilon Storage Division, EMC, Seattle

—Bob Nelsen, managing director, Arch Venture Partners, Seattle

So if you haven’t already, register here mark your calendars for the afternoon of February 7 for some thoughtful conversation and a rare networking opportunity between techies and biotechies. Hope to see you there on February 7.

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Most of the major life sciences reporters in the U.S. are gathered this week in San Francisco, so you know what that means—most of us missed the big story.

While pretty much everyone here at the JP Morgan Healthcare Conference—me included—was listening and learning about the latest hot new drug or device, the real news yesterday came from the world of super-fast, super-cheap gene sequencing. Mountain View, CA-based Complete Genomics (NASDAQ: GNOM) said yesterday it has agreed to sequence 615 complete human genomes for the Institute for Systems Biology, the nonprofit research center in Seattle led by biotech pioneer Leroy Hood. The Institute wants the genomes for its research into neurodegenerative diseases.

Not to be outdone, San Diego-based Illumina (NASDAQ: ILMN), the market leader in gene sequencing instruments, unveiled its latest iteration. This tool, dubbed MiSeq, is a desktop-sized sequencing machine that can be bought for about $125,000, a fraction of previous devices’ costs, and do a lot of heavy duty sequencing for a few hundred bucks per run. It’s a direct answer to the aggressive move of its competitor, Carlsbad, CA-based Life Technologies (NASDAQ: LIFE), which has generated a lot of buzz lately with its cheap and fast new tool it acquired from Ion Torrent Systems.

I don’t really have time today to let these moves sink in, because it’s kind of rude to bail out on meetings scheduled weeks ago. I can always follow up for Xconomy readers later. But it’s worth remembering that it took $3 billion and about 13 years just to sequence one genome, and as of a couple years ago, it was so expensive and time-consuming, only about a dozen or so complete genomes were sequenced. Today, a company tells the world it will sequence 615 complete genomes for a single customer, and Wall Street gives it a paltry 5 percent stock lift, and reporters Tweet and move on. There are certainly huge computing challenges in managing all this data, and no guarantee that biologists will figure out how to do anything useful will all this new information on what’s happening in individual people at the genomic level. But days like yesterday remind me that a mentor once told me that a journalist ought to be skeptical, yet never lose his sense of wonder.

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‘Twas the week before JP Morgan and all through the house…OK you get the idea. Not much biotech news was stirring this week as everybody is prepping for the big industry confab next week in San Francisco. I’ll be reporting there as always.

—We rang in the New Year on the biotech desk with a story titled “The Immunex Alumni: Where are they now?” It’s been more than eight years since the Seattle biotech bellwether was bought by Amgen, so I thought it would be interesting to track down where a lot of the Immunoids went. I’m getting a lot of great comments in my inbox, and please keep them coming. The list has 306 names at last count, and if you or someone you know is an alumnus that would like to be included, just send me a note at ltimmerman@xconomy.com

—One of the most prominent Immunex alumni, Doug Williams, made some news this week when he took a new job as the executive vice president of R&D at Weston, MA-based Biogen Idec (NASDAQ: BIIB). This means Seattle biotech can subtract one of its few bankable CEO candidates, as Williams is headed off to the East Coast.

—AVI Biopharma (NASDAQ: AVII), the Bothell, WA-based developer of RNA-targeted therapies, said it has formed an alliance with the Karolinska Institute in Sweden to look for new drugs against extensively drug resistant forms of tuberculosis. Financial terms weren’t disclosed, but the two parties will split research costs.

—Seattle-based Omeros (NASDAQ: OMER) said it has obtained an exclusive license from the University of California to a number of new drug candidates for trauma-related and surgical bleeding. Terms weren’t disclosed.

—Genentech, the biotech giant in South San Francisco, has taken a license to a number of antibacterial drug candidates from AMRI, the pharmaceutical service firm. AMRI did much of the work on these novel compounds, derived from natural product sources, at its lab in Bothell, WA.

—Leroy Hood added another major prize to his trophy case this week. Hood took home the Russ Prize, a $500,000 bioengineering honor presented by the National Academy of Engineering. Hood won for his most famous series of inventions in high-speed gene sequencing, which laid a critical foundation for the Human Genome Project and the wave of faster/cheaper genome sequencing that came after.

—We have had a bunch of guest editorials flowing into the Xconomy Forum lately, on a number of tech-related themes, and from a number of writers in our 5-city network. Here are two from the past couple weeks that are of most interest to Seattle biotech readers. Sue Siegel, a partner with Mohr Davidow Ventures, offered her view on five things to watch for in the coming year of healthcare and life sciences. And Larry Corey, the new president of the Fred Hutchinson Cancer Research Center, provided his thoughts on how vaccines were the big innovation story he saw in 2010.

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Leroy Hood, the pioneer of high-speed gene sequencing machines, has added another big item for his trophy case. Hood has won the Fritz J. and Dolores H. Russ Prize, a $500,000 award for bioengineering achievement that is presented by the National Academy of Engineering. Hood has previously received a number of prestigious honors, including the Lasker Award, the Kyoto Prize, and the Lemelson-MIT Prize for Invention and Innovation.

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The quest to sequence entire human genomes for $1,000 or less is one of the stories that many predict will change healthcare in the 21st century. It’s an enormously complex puzzle that requires some of the brightest minds in both IT and life sciences to put their heads together. And quite a few of them are working to make this happen right here in Seattle.

So that’s why I’m pleased to announce we’re adding a couple more great speakers to our next event, “Computing in the Age of the $1,000 Genome” on February 7th in Seattle. The first is Paul Rutherford, the chief technology officer of Seattle-based Isilon Systems, which has now officially been acquired by EMC for $2.2 billion. The second is Bob Nelsen, the managing director of Arch Venture Partners, an early investor in Illumina, the leading maker of DNA sequencing instruments that are creating this massive data pile-up.

Rutherford is a natural fit for this event because he has spearheaded Isilon’s work in providing the immense data storage capability that biologists need when they run DNA sequencers that spit out billions of data points. Isilon has gotten some early traction in this market, having signed up A-list customers like The Broad Institute of MIT and Harvard, Johns Hopkins University, Merck, & Genentech.

Rutherford will offer his perspective during a panel at this event alongside Deepak Singh of Amazon Web Services, and Jim Karkanias of Microsoft Health Solutions. Each comes at the genomic data challenge from a slightly different angle—Amazon is focused on flexible cloud computing approaches for storage and analysis, Microsoft has an open-source software platform it is pushing along with bioinformatics software to crunch the data, while Isilon offers hard core centralized servers to store and access the data at places that pump out vast amounts of DNA sequences every day.

I’ve asked Tim Hunkapiller, one of the founding fathers of bioinformatics from the early 1980s at Caltech, to moderate this panel. Hunkapiller has a long history as an academic scientist, and these days has his finger on the pulse of what’s new in DNA sequencing instruments, partly through his work as a consultant to one of the industry leaders, Carlsbad, CA-based Life Technologies (NASDAQ: LIFE).

Paul Rutherford

Nelsen, who’s never afraid to stir the pot, will join this event for a closing fireside chat with biotech pioneer Leroy Hood.

So, here’s the updated list of speakers:

—Leroy Hood, the co-founder and president of the Institute for Systems Biology, Seattle

—Cliff Reid, co-founder and CEO, Mountain View, CA-based Complete Genomics

—Eric Schadt, chief scientific officer, Menlo Park, CA-based Pacific Biosciences

—Jim Karkanias, senior director, applied research and technology, Microsoft Health Solutions, Redmond, WA

—Deepak Singh, senior business development manager, Amazon Web Services, Seattle

—Rowan Chapman, partner, Menlo Park, CA-based Mohr Davidow Ventures

—Andreas Sundquist, co-founder and CEO, Palo Alto, CA-based DNANexus

Bob Nelsen

—Ilya Kupershmidt, co-founder and VP of products, Cupertino, CA-based NextBio

—Rob Arnold, president, Seattle-based Geospiza

—Tim Hunkapiller, Seattle-based consultant, Life Technologies

—Paul Rutherford, chief technology officer, Isilon Systems, Seattle

—Bob Nelsen, managing director, Arch Venture Partners, Seattle

Tickets have been going fast for this event, and at the current pace I wouldn’t be surprised if this event sells out a couple weeks in advance. So check your calendars for the afternoon of February 7, and join us for a thoughtful conversation about how computer scientists can work with biologists in a way that will ultimately shake up medicine as we know it.

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An incredible innovation story has been unfolding the past few years in DNA sequencing, giving rise to one of today’s grand challenges of computing. New DNA sequencing tools in development are said to have enough horsepower to decipher the complete 3-billion-letter signature of an individual’s DNA for under $1,000, and possibly with as little as 15 minutes of crunching. If this can truly be done on a large scale, scientists say it could clear the way for a more personalized brand of medicine.

We are fortunate in Seattle to live in one of the few places on Earth with the necessary cluster of computing and life sciences talent that it will take to put together this puzzle. That’s why I’m thrilled to say today that Xconomy will bring together world leaders from the Northwest, and from the San Francisco Bay Area, for a truly special half-day summit on February 7 called “Computing in the Age of the $1,000 Genome.”

This will be a star-studded event from beginning to end, featuring interactive conversations with scientists, entrepreneurs, and investors. Here’s the lineup of confirmed speakers.

—Leroy Hood, the co-founder and president of the Institute for Systems Biology, Seattle

—Cliff Reid, co-founder and CEO, Mountain View, CA-based Complete Genomics

—Eric Schadt, chief scientific officer, Menlo Park, CA-based Pacific Biosciences

—Jim Karkanias, senior director, applied research and technology, Microsoft Health Solutions, Redmond, WA

—Deepak Singh, senior business development manager, Amazon Web Services, Seattle

—Rowan Chapman, partner, Menlo Park, CA-based Mohr Davidow Ventures

—Andreas Sundquist, co-founder and CEO, Palo Alto, CA-based DNANexus

—Ilya Kupershmidt, co-founder and VP of products, Cupertino, CA-based NextBio

—Rob Arnold, president, Seattle-based Geospiza

—Tim Hunkapiller, Seattle-based consultant, Life Technologies

Of course, this wouldn’t be a realistic conversation without talking about the barriers standing in the way of a future based on genomic medicine. There are still immense challenges to be confronted before this vision can become reality. For starters, the genomic data will need to be stored, secured, backed up, analyzed, and visualized in order for it to live up to its promise.

Still, many of today’s high-tech leaders, including Amazon and Microsoft, see big opportunities in helping overcome those challenges through their cloud computing technologies. And while an earlier generation of entrepreneurs struggled to build businesses around software for managing genomic data, a new wave of startups is emerging to tackle the challenge anew.

This without question will be one of the biggest innovation stories in the world over the coming decade, with the potential to forever change the way we think about health and wellness. It’s often said that we as journalists get a front row seat to history in the making. I feel like this is one of those moments, and I feel privileged to invite you to come meet the newsmakers in person, and to pepper them with a few questions of your own about how this is supposed to go from concept to reality.

This event will take place from 2 pm to 6 pm on Monday, February 7, at Swedish Medical Center’s James Tower Auditorium. You can find more information and reserve a seat here at the registration page. See you there on February 7.

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Nathan Myhrvold is a physicist who made his name as a software guy at Microsoft. So it’s natural to think that if his Bellevue, WA-based invention firm, Intellectual Ventures, creates anything of lasting value, it will probably come from physics or software. Maybe it will be something really offbeat (fighting infectious disease with mosquito-zapping lasers), or really big and audacious (cheap, clean nuclear power at TerraPower).

But a couple of new dealmakers that Intellectual Ventures has hired in the past six months say some of the company’s biggest inventions could come from a surprising sector—medical devices. These could be things as simple as efficient new bone screws, safer and more vivid medical imaging devices, new drug discovery technologies, diagnostics, or touchscreen interfaces embedded with technology to automatically kill viruses and bacteria circulating in the environment.

“We have thousands of inventions in the medical technology space that were conceived of by our team of inventors. Literally, thousands,” says Daniel Hawkins, the new vice president of business development at IV, responsible for medical technologies. “The medical device universe is just starting to hear from us.”

Intellectual Ventures has its share of critics, who see it as little more than a patent troll that goes around scooping up intellectual property and then forcing innovators to cough up cash or else get sued for infringement. The firm naturally bristles at this criticism, and counters by arguing that it actually creates a lot of inventions in-house (and that it hasn’t ever sued anyone). Part of this comes through brainstorming “invention sessions” where it brings in superstar scientists like MIT’s Robert Langer and Leroy Hood of the Insitute for Systems Biology to invent stuff. The value of all this inventing is hard to pin down on a spreadsheet, because no one knows what will pay off in the marketplace and what won’t in the future. But IV has grown to the point—with more than $5 billion under management and more than 700 employees worldwide—that it’s time to start showing its investors it can apply inventions to real-world problems and generate returns.

That’s where Hawkins and his colleague Paul Duesterhoft enter the picture. Hawkins, a seasoned medical device entrepreneur, previously worked in a couple of venture-backed startups incubators—one that’s now become Calibra Medical, the maker of a miniature insulin delivery pump, and another called Aspen Medtech, which closed down a year ago. Duesterhoft was formerly a vice president of marketing at Seattle-based ZymoGenetics (NASDAQ: ZGEN). They have both been hired in the past six months at IV, as the first businesspeople charged with sorting through the company’s medical tech portfolio of patent applications and potential patent applications, to see which ones may become real products. That means figuring out what’s valuable to the Johnson & Johnsons, Boston Scientifics, and Medtronics of the world, and striking some deals to license technology to them. Maybe, once in a while, this might even lead to the creation of a new company.

Intellectual Ventures hasn’t talked publicly about … Next Page »

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Lee Hartwell would be excused if he wanted to rest on his laurels at the age of 70 and enjoy the sort of retirement that you read about in personal finance magazines. Instead, he’s now setting out to do the most ambitious things of his career. He wants to change the way the world thinks about personalized medicine, help make the world a more sustainable place, and improve how children learn about science.

“I’m not a person who looks back,” Hartwell says. “I don’t tend to miss things. I look upon each stage as an experience and a learning opportunity. I came into this to learn about medicine, and it was an enormously powerful experience. Now it’s time to move on and use that knowledge.”

Hartwell made his name as a basic scientist; his fundamental discoveries about cell processes in yeast earned him the 2001 Nobel Prize. Then as the president and director of the Fred Hutchinson Cancer Research Center in Seattle, he oversaw 13 years of growth and integration between basic science, clinical practice, and public health. Now that Larry Corey has been tapped as his successor, Hartwell is preparing for his next major challenge: chief scientist of The Biodesign Institute at Arizona State University, starting Oct. 1. He told me about his vision for the next chapter of his career when I recently visited his office in Seattle.

His vision is to create a new wave of precise and predictive diagnostic tests, based on systematic analyses of all sorts of proteins in the blood that could be early warning signs of disease. These tests will enable physicians to answer basic problems, like determining when an emergency-room patient’s chest pain is just garden-variety or an early warning sign for a heart attack or stroke. Armed with that kind of individualized knowledge, physicians would be able to make more informed decisions about patient care, saving resources that are currently wasted.

Many people see this as essential to fixing healthcare in the future, but Hartwell is looking through an even wider societal lens. He talks about how this more efficient model of healthcare will help the world focus resources on global sustainability, like clean air, clean water, or as he puts it, “maintaining the planet in a way that will continue to support human life.” One part of that vision, for which he plans to devote half of his time, will be about improving K-8 science education. Done right, it could help foster a new generation of more scientifically literate citizens who will help support those initiatives.

One of Hartwell’s peers, Leroy Hood of the Institute for Systems Biology in Seattle, said he expects big things from Hartwell’s new mission. Hartwell, he says, “approaches the … Next Page »

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We had some noteworthy personnel moves, a big real estate deal, and some legal battling on the biotech beat this week.

—The Institute for Systems Biology made it clear early this year it was scoping out the former Rosetta Inpharmatics building in South Lake Union as its future home, and this week the nonprofit research center made it official. Biotech pioneer Leroy Hood says he’s eager to get his whole team back under one roof, and to be within walking distance of so many other top-notch biologists in South Lake Union. He might even be able to walk to work on nice days.

—A smaller, but interesting biotech real estate move is happening over at a legendary address—1100 Olive Way. Seattle Children’s Research Institute is taking over the space once occupied by gene therapy leader Targeted Genetics, with an eye toward turning it into a hotspot for pediatric cancer research.

—Sometimes innovation stories can lead to unusual places, and this week I found an interesting story in the world of healthcare delivery. Tacoma, WA-based Sound Physicians has built a thriving business on offering services of hospital-based physicians who are focused on evidence-based medicine, and are supposed to be able to save hospitals a few percentage points on their operating margins, while enabling private practice doctors to stick in their offices and do their thing.

—An interesting trademark dispute has flared up between a couple of Seattle-area biotechs that are seeking to become bigger players in the field of RNA-based therapies. Mirina, a two-year-old startup that’s incubating at the Accelerator, has brought a federal trademark infringement suit against the company that used to be called Nastech Pharmaceutical, and used to be called MDRNA, and is now calling itself Marina Biotech. This new name is bound to cause confusion in the market, Mirina argues.

—SonoSite (NASDAQ: SONO), the Bothell, WA-based maker of portable ultrasound machines, said its founding chairman, Kirby Cramer, is retiring from that position he has held for 12 years. Cramer, 74, said he’s trying to practice the stuff he preaches to students at the UW Foster School of Business about how companies need to get new blood on their board after about 10 years.

—Seattle-based Trubion Pharmaceuticals (NASDAQ: TRBN) said it agreed to be acquired by Rockville, MD-based Emergent BioSolutions for about $97 million upfront, plus milestone payments. Emergent plans to keep a drug R&D center here in the Northwest, Trubion says.

—Calypso Medical Technologies, the Seattle-based maker of technology to pinpoint radiation therapy for prostate cancer patients, said it formed a European distribution deal with Siemens Healthcare.

—Blue Heron Biotechnology, the Bothell, WA-based maker of customized genes that biologists can use in their labs, said it agreed to be acquired by Rockville, MD-based Origene Technologies. Terms weren’t disclosed.

—Seattle-based Allozyne, the developer of modified protein drugs, said it secured a technology license from chemical giant Sigma-Aldrich which will give it more flexibility in how it chooses to modify its protein drug candidates.

—And last, I had a piece with both Silicon Valley and Northwest connections—a profile of ZeaChem. This company, which has labs in Menlo Park, CA, and a major demonstration plant along the Columbia River in Boardman, OR, is putting its ethanol-from-wood-chips concept to the test in a big way this year in Oregon. We’ll be eager to see how that pans out.

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The worst kept secret in the local biotech real estate market is now official: The Institute for Systems Biology is moving to Seattle’s South Lake Union neighborhood, into the modern building once occupied by Merck’s Rosetta Inpharmatics unit.

Leroy Hood, the biotech pioneer who heads up the Institute for Systems Biology, told me back in March that he had set his sights on the Rosetta building for his future growth plans. Now the Institute has signed a lease there on 140,000 square feet of space at 401 Terry Avenue North, which has enough room to house 330 employees starting in the spring of 2011.

The nonprofit Institute for Systems Biology has been bursting with growth the past couple of years, and outgrew its labs and offices near Gas Works Park on the north side of Lake Union. The Institute lives mostly off its ability to win competitive federal research grants—which can be a tenuous existence—but the Institute has gotten financially strong enough over the past couple years to make a move on a bold property like the former Rosetta building that was developed by Paul Allen’s Vulcan Real Estate.

A turning point for the Institute came in June 2008 when it secured a five-year, $100 million commitment from the government of Luxembourg to test Hood’s vision of “P4 Medicine,” which stands for predictive, preventive, personalized, and participatory. In January, an independent review of research institutes around the world said the Institute for Systems Biology produced the highest impact scientific publications of any U.S. research center from 2003 through 2007. And in March, the Institute said it received a $6 million gift from an unnamed California venture capitalist to further its research in personalized medicine, biofuels, and global health.

The Institute’s annual budget has grown to about $50 million this fiscal year, and it expects to have about 500 employees within 10 years.

“The Terry Avenue North building more than doubles our current space, permits us to consolidate employees under one roof, and provides easy access to some of the most effective research institutions in Washington state,” Hood said in a statement. “It will also enable us to acquire new faculty with critical skills in systems science (biology, medicine, technology and computation/mathematics), as well as provide the space for future growth and the creation of new strategic partnerships.”

Leroy Hood

For those who follow the local real estate scene, this puts the Institute closer to the heart of the action, at least in billionaire Paul Allen’s vision for the future of the city. The Institute will be walking distance from Seattle Biomedical Research Institute; PATH, the nonprofit global health catalyst; the Fred Hutchinson Cancer Research Center; Novo Nordisk‘s inflammation research center; Amazon‘s new headquarters; the University of Washington’s branch campus loaded with stem cell researchers, and the Accelerator, the biotech startup machine that maintains close ties with the Institute for Systems Biology.

It’s a homecoming in a way. Hood was a co-founder of Rosetta Inpharmatics in 1996, along with Stephen Friend and Lee Hartwell. Friend led the operation from its beginnings at an office park in Kirkland, WA, took it public, and sold the company to Merck in 2001 for more than $600 million. Merck lavished resources on the Rosetta operation for years, saying its insights into gene expression and computation could help the pharma giant screen out winners from losers early in the drug development process, and possibly help researchers get the right drug to the right patients. Merck set up Rosetta in the multi-million facility developed by Vulcan and Schnitzer West in 2004, and eventually employed about 300 people there. But Merck pulled the plug on its Rosetta operation as part of global budget cuts in the fall of 2008, announcing plans to move some of its researchers to other locations, and close the Seattle facility.

I’m scheduled to talk with Hood later this morning and will update this space shortly after.

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This week, we saw more than the usual number of venture deals on the Seattle life sciences beat. Maybe the VCs needed to tie up some loose ends before unplugging in the month of August.

—Seattle-based Immune Design snagged the big round of the week, a full $32 million Series B deal that included ProQuest Investments, Alta Partners, Versant Ventures, and The Column Group. The company, led by Corixa co-founder Steve Reed, is following that same tried-and-true formula for company building, Reed told me in an exclusive follow up interview.

—Integrated Diagnostics, the Seattle-based company co-founded by biotech pioneer Leroy Hood, secured a $10 million second installment of a Series A venture financing round first announced in October. The company hit a series of milestones on its quest to develop a test that will take a pinprick of blood and use it to predict the odds that a person will get lung cancer, or even Alzheimer’s.

—HemaQuest Pharmaceuticals tacked on an additional $4 million to its Series B round, bringing the total value of that deal to $16 million. The Seattle-based company, led by CEO Ron Berenson, is developing treatments for sickle cell anemia, and a lymphoma related to infection with Epstein-Barr virus.

—SonoSite (NASDAQ: SONO) is always thinking of some new way for doctors to use ultrasound as a diagnostic tool, and last week I experienced one of those uses first hand. The company is seeking to get more primary care doctors to use ultrasound scans of people’s carotid arteries, to see how much plaque is building up, which can be an indicator of future risk of heart attack or stroke. Fortunately, the company sonographer says I won’t be keeling over anytime soon.

—Marina Biotech, the Bothell, WA-based company formerly known as MDRNA and Nastech Pharmaceutical, secured some intellectual property to help it deliver RNA-based therapies inside cells. Marina (NASDAQ: [[MRNAD]]) paid $5 million worth of common stock to get the RNA delivery technologies from Germany-based Novosom.

—We had a couple of sharp guest editorials from contributors outside the Northwest who nonetheless made points that are relevant to the biotech community here. Steve Speer, a biotech consultant in Carlsbad, CA, wrote a guest post about why penny-pinching isn’t necessarily the best way to get bang for the investor buck at a biotech startup. And Daniel MacArthur, a top-notch genomics blogger and researcher at the Wellcome Trust Sanger Institute in the U.K., talked about how direct-to-consumer genetics companies like 23andMe took a public flogging at a congressional hearing last week, and how this could harm the future cause of research and personalized medicine.

I know you Seattleites have opinions too, so if you’ve got something relevant to the local innovation community that you’d like to say, shoot me a note at ltimmerman@xconomy.com. I’ve been known to help quite a few shy writers with some editing, and they tell me it’s not as bad as a trip to the dentist.

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