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Paul Allen’s new cell-science institute will share more than a building with the brain-research center the Microsoft mogul established in his hometown 11 years ago.

Both facilities were created to tackle problems in biology so complex they are beyond the reach of individual scientists. Both bring together experts across a wide range of disciplines. And both aim to push the boundaries of medicine through fundamental discoveries.

The budget numbers are pretty similar, too.

On Monday, Allen announced he is donating $100 million over five years for the Allen Institute for Cell Science in Seattle. That’s the same initial amount he committed to the Allen Institute for Brain Science in 2003. Since then, Allen has invested $400 million more, increasing the staff to 350 people and making the brain institute his single largest philanthropic effort.

The cell institute could follow a similar trajectory if it is able to make progress toward unraveling the inner workings of human cells, said Allan Jones, who leads the brain institute and helped organize the new initiative.

“We need to knuckle down and show that we can deliver something very powerful,” Jones said.

The long-term goal of the new institute is to better understand the teeming world inside cells, where thousands of organelles and millions of molecules interact in a dynamic ballet that researchers are just beginning to fathom.

“We really don’t have a good idea of how normal cells work, and what goes wrong in disease,” said Rick Horwitz, the former University of Virginia professor who jumped at the chance to lead the new institute. “People spend careers trying to understand little parts of the cell, but nobody has stitched it together — because it’s too complicated for any individual to study.”

The institute will take on the challenge by combining new technologies, such as microscopes that can visualize living cells in three dimensions, with enough computational firepower to make sense of the flood of data that will result, Horwitz said.

He and his team hope to develop computer models that mimic living cells. If they succeed, those models could shed light on what goes haywire in cancer and other diseases and help develop cures.

“Cells are the battleground for every disease known to humans,” Jones said.

With a fortune estimated at $17.1 billion, Allen ranks 44th on Forbes’ list of the world’s richest people.

After joining his old Microsoft partner Bill Gates in pledging to donate the bulk of his wealth, Allen has accelerated his giving in recent years, targeting causes as varied as elephant conservation and ocean health.

This fall, he committed $100 million to fight the Ebola epidemic in West Africa.

Allen’s $100 million infusion for cell science is among his largest grants. Coming at a time when federal research budgets are shrinking, the announcement is “one of the most exciting things to happen in Seattle science in a long time,” said Dr. Chuck Murry, co-director of the Institute for Stem Cell and Regenerative Medicine at the University of Washington. “When the Allen folks get into something, they do it at a scale that’s just mind-blowing.”

Allen’s interest in cell biology grew out of his long-standing fascination with complex systems, Jones said. He also saw a need for the type of big science approach that’s rare in biology.

While diagrams in textbooks make it seem like cell structure and function have already been nailed down, that’s far from true.

Scientists have indeed learned a lot about different cell types, the role of organelles like the nucleus, and specific pathways, such as the chain of events that causes muscle cells to contract. But there’s a big gap when it comes to understanding the way cells function as a whole.

For example, researchers tried and failed for years to coax breast-tissue cells growing in petri dishes to produce milk proteins. What finally worked was growing the cells on a pliable matrix, more like their natural habitat.

“All these nuances are really important,” Horwitz said.

One reason it has proved so difficult to translate genetic discoveries into treatments is that scientists have only a fuzzy idea of the way gene mutations upset the normal cellular machinery.

Applied on a large scale, super-resolution microscopy along with techniques to precisely tweak DNA and tag molecules with fluorescent dyes will allow researchers at the institute to track what’s happening inside normal cells and see what changes when mutations are introduced, Horwitz said.

The result will be like Google Maps for cells, he added. “Our output will be a kind of visual, dynamic atlas that shows where all of these things are in the cell and how they change over time.”

The first project will focus on the way stem cells derived from adult tissue transform themselves into multiple cell types, including heart muscle and skin.

Understanding that process in more detail will be of great value in the effort to harness stem cells to repair damaged organs, said Jennifer Lippincott-Schwartz, president of the American Society of Cell Biology.

Horwitz and Jones unveiled plans for the institute Monday at the society’s annual meeting in Philadelphia.

“We’re all very excited about this initiative,” Lippincott-Schwartz said.

With its dedicated mission, the cell institute will be able to assemble experts in cell biology, computational modeling and microscopy in a way that’s tough to do at a university, said Joan Brugge, chairwoman of the Department of Cell Biology at Harvard Medical School.

“You need a really coordinated effort,” said Brugge, who serves on the institute’s science advisory board. “It’s very difficult for the federal funding agencies to fund these kind of Manhattan Project-style initiatives, because they are so large.”

Just as at the Allen Institute for Brain Science, all of the data and tools developed at the cell institute will be freely available to scientists around the world.

The two institutes will be housed together in a new, seven-story lab building under construction in the South Lake Union neighborhood.

The cell institute will build up to a staff of about 75 scientists, technicians and other staff in its first few years, Horwitz estimated.

Sandi Doughton at: 206-464-2491 or sdoughton@seattletimes.com