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When news that the brand-new startup Ophthotech had raised a $36 million first round broke on Monday, it was clear that the venture amounted to a kind of do-over for officials of the late, unlamented Eyetech Pharmaceuticals. Eyetech, you might recall, burst onto the scene with a rocket-science aptamer-based blindness drug called Macugen and a flashy $157 million IPO, then proceeded to get its head handed to it by even better rocket science from Genentech, and eventually sold itself ignominiously to OSI Pharmaceuticals for a lower share price than its IPO (a deal that apparently worked out even less well for OSI).

I didn’t write any of this at the time, however, and in the meantime several others have made a number of interesting observations about Ophthotech’s emergence, not to mention noting some eerie historical parallels. Fred Cohen at Pharma’s Cutting Edge offered this acerbic interpretation:

OSI is now divesting its eye business. As part of the divestiture, OSI has licensed its apatemer targeting PDGF (a related angiogenic peptide) to newly formed Ophthotech. Ophthotech has also licensed development and marketing rights to Archemix’s aptamer targeting the C5 component of complement (an inflammation factor). As you’ll read, Ophthotech is staffed largely by former Eyetech execs. It’s a chance for them to do it all over again. Perhaps this time around they will not sell out the early public-market investors by dumping the firm below its IPO price, while reserving a tidy sum for themselves.

But to really head through the looking glass, you have to turn to the In Vivo blog, where Chris Morrison writes:

SV Life Sciences, HBM BioVentures, and Novo AS have just funded an ophthlamology start-up with a $36 million Series A that will pay for the acquisition of two interesting drug candidates. Didn’t that happen last year? It sure did, in May 2006. The company was Lux BioSciences.

OK, how about this: David Guyer, MD, and Samir Patel, MD, have teamed up as founders of an ophthalmology specialist based on in-licensed aptamer drugs and hope to make headway in the tricky macular degeneration space. SV (then Schroder Ventures Life Sciences) was an early investor. No, no, no, that was way back in 2000. Eyetech, right? Absolutely.

Guyer is now chairman of Ophthotech and Patel is CEO. Morrison goes on to note that Ophthotech has licensed an aptamer against platelet-derived growth factor from none other than OSI, which, of course, originally acquired it from… Eyetech. A second deal brought in more aptamers from Archemix (see our coverage), which bought Gilead Sciences’ aptamer technology in 2001, gaining control of everything but… the aptamer that Gilead licensed to Eyetech, which became Macugen.

Morrison rightly wonders why all the technology and money now flowing into Ophthotech didn’t go to Lux BioSciences instead. The answer, he suggests, may simply be that Big Pharma’s hunger for biotech — and its tendency to pay top dollar — has convinced VCs that they’re better off spreading their eggs among as many baskets as possible.

Or, as Morrison puts it:

Oddly enough, only a few years ago, it would have been a sure thing to keep all these assets under one corporate roof, because the VCs would have been hoping for an IPO exit, and investors like to see multiple clinical projects at IPO hopefuls. Now that M&A is the preferred exit, the assets are siloed. For now.

(UPDATED at 5:55pm PT: See below.)

Featured companies: Sierra Surgical Technologies, HerbalScience Nutraceuticals, Topigen Pharmaceuticals, EKR Therapeutics, Molecular Partners, Celsense, Glucose Sensing Technologies, Falcon Genomics, Waters, Calorimetry Sciences, Parion Sciences, Gilead Sciences, Isto Technologies, Fluidnet, NABsys

Sierra Surgical raises $7.1M — Palo Alto, Calif.-based Sierra Surgical Technologies, a developer of female sterilization technology, raised $7.1 million in a first funding round, PE Hub reports, citing a regulatory filing. Alta Partners and De Novo Ventures provided the funding.

Singapore’s HerbalScience raises $28M for natural extracts — HerbalScience Nutraceuticals, a Singapore-based natural-extracts company with offices in Naples, Fla., raised $28 million from the private-equity firms Aisling Capital and Weston Presidio, VentureWire reports (subscription required). The investment purchased a 25 percent stake in HerbalSciences, which makes purified extracts from various natural substances, valuing the company at $112 million.

Topigen Pharma pulls in $25M against lung disease — Montreal’s Topigen Pharmaceuticals, a biotech developing inhalable drugs to treat asthma and other lung diseases, raised $25 million (C$26 million) in a third funding round. Investors included NovaQuest, MMV Financial, BDC Venture Capital, Desjardins Venture Capital, Caisse de Dépot et Placement du Québec (Caisse), T2C2/BIO 2000 and Lothian Partners 27 (sarl) SICAR.

The funding will “accelerate” mid-stage human trials for Topigen’s leading drug candidates, a small-molecule treatment for chronic obstructive pulmonary disease and an RNA inhibitor for asthma.

EKR receives over $13M, licenses opiod drug — EKR Therapeutics, a Cedar Knolls, N.J., specialty pharmaceutical company, raised more than $13 million in a private placement. Investors included Quaker BioVentures, NewSpring Capital, and ESP Equity Partners. EKR also acquired rights to DepoDur, an extended-release opioid, from Pacira Pharmaceuticals.

Switzerland’s Molecular Partners gets $15.6M for novel binding proteins — Zurich-based Molecular Partners, a biotech developing drugs based on a new class of binding proteins, raised $15.6 million (CHF18.5 million) in a first funding round. Investors included Index Ventures, BB Biotech Ventures, Johnson & Johnson Development Corp. and Endeavour.

Molecular Partners is focused on developing therapeutics proteins it calls “DARPins,” which the company says offer the same ability to stick selectively to other molecules as monoclonal antibodies, but with greater stability and ease of manufacturing. DARPins are based on the notion of “repeat proteins,” which as the name suggests are modular proteins that contain repeated elements — something like posts spaced at regular intervals along a barbed-wire fence. (See the image at left.) The protein itself ends up looking something like a string that’s been knotted at regular intervals, only much more complicated.

Repeat proteins are found in almost all species, and in nature serve to bind other proteins in order to facilitate protein-protein reactions. By shuffling the modular elements in these proteins, they can be engineered to stick to specific molecules such as cell-surface proteins, potentially making them useful as drugs. The company has a more detailed description here.

Although Molecular Partners likes to play up the advantages of DARPins (the acronym stands for “designed ankyrin repeat proteins”) over antibodies — here, for instance — there are a few disadvantages the company doesn’t mention. As large molecules, DARPins most likely won’t get inside cells, limiting their potential as drugs to interactions with free-floating and cell-surface proteins. (Monoclonal antibodies have the same limitation.) Potentially more important, however, is the fact that the effectiveness of many antibody-based drugs results from their ability to stimulate a particular immune response, not just to stick to the appropriate target. DARPins, which aren’t immune-system molecules the way antibodies are, seem unlikely to do the same.

Pittsburgh-area biotechs, device makers get $350K — The Pittsburgh Life Sciences Greenhouse, a public-private life-sciences investment partnership, invested $350,000 in three Pittsburgh-area life-science startups. Falcon Genomics, a developer of chip-based cancer-detection diagnostics, received $150,000. Another $100,000 went to Celsense, which uses an MRI tracing agent to image transplanted cells. The final $100,000 was invested in Glucose Sensing Technologies, which is developing a catheter-based glucose sensor for continuous blood-sugar monitoring in intensive-care units.

Waters acquires Calorimetry Sciences — Milford, Mass.-based Waters, a laboratory-instrument maker, acquired Calorimetry Sciences of Linden, Utah. Terms of the deal weren’t announced. Calorimetry Sciences, which makes high-performance devices intended to measure the heat produced or absorbed by chemical reactions, will be merged into Waters’ TA Instruments division.

Fedora Commons wins $4.9M grant for open collaboration software — Fedora Commons, a non-profit organization devoted to open-source technologies for creating and sharing digital content, received a $4.9 million grant from the Gordon and Betty Moore Foundation. From the release:

With this funding, Fedora Commons will foster an open community to support the development and deployment of open source software, which facilitates open collaboration and open access to scholarly, scientific, cultural, and educational materials in digital form. The software platform developed by Fedora Commons with Gordon and Betty Moore Foundation funding will support a networked model of intellectual activity, whereby scientists, scholars, teachers, and students will use the Internet to collaboratively create new ideas, and build on, annotate, and refine the ideas of their colleagues worldwide. With its roots in the Fedora open-source repository system, developed since 2001 with support from the Andrew W. Mellon Foundation, the new software will continue to focus on the integrity and longevity of the intellectual products that underlie this new form of knowledge work. The result will be an open source software platform that both enables collaborative models of information creation and sharing, and provides sustainable repositories to secure the digital materials that constitute our intellectual, scientific, and cultural history.

Parion licenses lung-disease drug to Gilead for up to $146M — Parion Sciences, a Durham, N.C., biotech focused on diseases of the mucous membranes, struck a licensing and co-development deal with Gilead Sciences for its drug P-680 worth up to $146 million. The drug, an epithelial sodium-channel inhibitor, could potentially be useful in a variety of lung diseases, including cystic fibrosis. The companies will also work to identify other similar drug candidates.

Isto Tech raises $8.8M, prepares to launch synthetic bone grafts — St. Louis’ Isto Technologies, a developer of cell-based cartilage and bone regeneration technology, raised $8.8 million in a fifth funding round as it prepares for its first product launch, VentureWire reports. Investors included Ascension Health Ventures, Alafi Capital, Life Sciences Partners, Mid-America Transplant Services and private individuals. Isto’s leading product, InQu, is a synthetic biomaterial intended to help tissues heal and bones to regenerate; Isto expects FDA approval later this year.

Fluidnet rises from ashes, raises $6.4M for IV pumps — Portsmouth, N.H.-based Fluidnet, a “reincarnation” of its bankrupt predecessor FluidSense, raised $6.4 million in a first funding round to launch a new intravenous-infusion pump next year, VentureWire reports. Cardinal Partners and Rockport Venture Partners provided the funding.

NABsys raises $750K for high-speed genome sequencing — NABsys, a Providence, R.I., startup focused on high-speed gene-sequencing technologies, raised $750,000 in seed funding, VentureWire reports. Slater Technology Fund and individual investors provided the funding, which closely follows a $1.3 million grant from the National Institutes of Health.

UPDATE (10:55am PT): Added items on Molecular Partners and the Pittsburgh Life-Sciences Greenhouse investments.

UPDATE REDUX (5:55 pm PT): Added items on Waters/Calorimetry Sciences, Fedora Commons, Isto Technologies, Fluidnet, NABsys.