The space shuttle is due to lift off on its final mission this week, and many scientists will cheer its departure, both from the planet and from the scene. The shuttle was key to the launch, repair and maintenance of the marvellous Hubble Space Telescope, but its contribution to science otherwise has been mediocre. Scientists often lament that the billions of dollars spent on the programme could have gone on robotic exploration of other planets, space telescopes and similar worthy causes. But they should not be too quick to welcome the demise of the shuttle. Its loss may foreshadow far darker times ahead for all space science.

The shuttle's scientific programme has never lived up to the hype. In its earliest days, programme advocates made outrageous claims that experiments in space might help to tackle HIV and cancer. Recent statements have been more measured and the science more peer-reviewed, but the flight schedule for Atlantis this week shows some dispiritingly familiar and low-quality space studies: a study of microbial virulence in zero gravity, experiments on weightless mice and an iPhone kitted out with International Space Station apps.

The shuttle was never about science, of course. The Nixon-era programme was designed to give NASA a purpose and, at the time, seemed to be the logical next step: a vehicle that could make fast and cheap excursions to the beginning of space. This has proved more difficult than expected. The programme never flew close to the 50 missions per year originally envisaged, and the cost per flight was always well above the estimates. Nor could the winged orbiter fly solo, depending instead on bulky boosters and its external fuel tank to give it an extra nudge into orbit — systems that were responsible for the catastrophic loss of Challenger in 1986 and Columbia in 2003. Each accident revealed flaws in both the design and the operation of the shuttle fleet.

Yet, despite its many shortcomings, it is wrong to condemn the shuttle as a snub-nosed albatross around the neck of research. Like it or not, the space shuttle is probably the most recognized symbol of science and technology for a generation. The shuttle programme was costly, but it kept NASA focused and in the thoughts of both Congress and the public.

The fear must be that without the shuttle programme, NASA and its strong space science will wither. The agency's flagship project, the James Webb Space Telescope, is desperately over budget and likely to be delayed for years. The next Mars rover is also seeing its costs skyrocket, and officials recently stalled plans for a US–European joint mission to the red planet because of mounting budget problems. Efforts to monitor Earth have stumbled with the loss of two high-profile climate satellites in as many years.

What is particularly unfortunate about this current state of affairs is that the possibilities for space science have never been greater. Space-based gravitational detectors could give researchers their earliest look at the Universe, and an array of space telescopes could provide insight into far-flung star systems. Closer to home, landers and rovers could teach us more about the Solar System's history and evolution, and Earth-observing satellites would improve our ability to understand and respond to climate change. Although none of these projects involves an astronaut, all require a strong and vital NASA to succeed.

Eventually, NASA may build another manned space vehicle to replace the shuttle, or it might find a mission that is more in line with the aspirations of the research community. But for now, it is an agency adrift.