Earth is spent, but the Universe awaits. It seems we can't get off the planet fast enough. Two thirds of Nasa's $17 billion annual budget is devoted to manned space exploration, a figure that will swell with President Bush's decision to send a man to Mars in 2037. We've seen all there is to see on Earth, right? Wrong. The final frontier is here. The deep sea remains unconquered even as its edges lap your beach towel.

Heading down into the ocean, human limits are quickly reached. At a depth of ten metres, the difference in pressure equals that between the Earth's surface and outer space. At 200 metres, the water is as black as a moonless night. By 300 metres the joints in our bodies are too compressed to move. Most nuclear submarines would implode before they reach 1km down, extinguished along with the last photons of light from the surface. Drop a fish hook to 3km - still less than the average depth of the ocean - and there's an even chance that you'll pull up a species completely new to science. The deepest-diving whales and their prey, the giant and colossal squid, go no farther. At the very bottom, more than 11km down, lie the Challenger Deeps. Twelve humans have walked on the moon. None has set foot in the Deeps, and only two have seen it with their own eyes.

Yet things live down there. Big things. Hydrophone arrays throughout the sea listen for the whisper of enemy submarines and can detect the exact frequency of propeller types. No one has explained the undersea roar that occasionally startles operators. The sound appears biological in origin, and its wavelength implies that it is produced by an animal bigger than a blue whale (the largest creature known on the planet).

An eminent Cambridge physicist dropped a deepwater probe in the Southern Ocean ten years ago, and passing 4,000 metres - well beyond the diving depth of any whale - it detected something enormous passing beneath it. Surprised? Don't be. The ocean covers 70 per cent of the planet's surface, and hosts 97 per cent of its biosphere. We've explored less than 5 per cent of it. We know far more about the dark side of the Moon than about the bottom of the sea.

One reason for exploring space is to find other life forms. The initial optimism of bolting gold-plated messages on to spacecraft has simmered down to passive listening while we scour planets and moons for evidence of water. There's no denying that the search for extraterrestrial life is important, but robots can look beneath the parched rocks of Mars better than humans. The idea of breaking through the upper atmosphere of an alien world and descending through the clouds to greet alien life is fantasy. For the real thing I'd suggest heading down in a deep-diving research submarine.

Except the UK doesn't have one. The US has only one: the 44-year old Alvin. It is due for replacement in 2011 but there are rumblings that the $22 million price tag is a problem. A single launch of the Space Shuttle costs $450 million, and buys only the morbid spectacle of astronauts risking death going to fix the already out-of-date International Space Station. The $700million that the US spends annually on marine research is only 4 per cent of its funding for space exploration. Without expensive manned space missions, the disparity in the UK - £100 million a year on marine research, £200 million on space - is less glaring, but ocean science is becoming reliant on remote sensing. This is a mistake - buoys, probes and satellites can only collect data for the questions they were designed to answer; our knowledge of the sea is still basic. To formulate questions we need more scientists making first-hand observations. We should bring funding for the marine science into line with space and send a new generation of Darwins off in undersea Beagles.

The engineering challenges stimulate technological development. The sea is a far more testing environment than space - the difference in pressure between the bottom and the surface is more than 1,000 times greater than that between the launch pad and Earth orbit. The enormous reserves of energy locked up in currents, waves and tides are a glittering prize. Teflon and new dimples on golf balls are impressive space-led innovations until compared with the biochemical reactions from benthic organisms that now constitute more than 50 per cent of our pharmaceutical anti-cancer arsenal.

Satellites and unmanned space probes allow us to communicate, look at our planet with a global perspective and stare into the history of the universe. They deliver most of the science that comes from the space programme, and are vital in ocean research too. But satellites can't peer under the sea, the only place where we can look for clues to the origin of life itself. To do that we need ships and submersibles (manned and robotic). The cost of fuel-intensive marine expeditions is rising, but the returns can directly benefit our lives.

Space attracts funding because we can see the stars. Astronauts who have returned from the Moon tell us (with crazed eyes) that Earth is a small oasis in an empty Universe and should be cherished. They see the world for what it is - a blue planet. With every important human indicator - population, food, energy - flashing warning lights, maybe it's time to take heed.

The sea is the most important factor in climate change because of its role as a heat sink and carbon store. Understanding the oceans is critical to ensuring protein, minerals and power. The threats (for example, asteroid strike) and opportunities from space are distant in comparison.

In 2010 it will be 50 years since Jacques Piccard and Don Walsh brought Swiss engineering and US finance together for their pioneering descent into the Challenger Deeps. Since the focus of our imagination turned to the heavens, no one has been back. With the increasing militarisation of Space, perhaps the time has come for nations to unite in a new era sea of exploration. Forty years ago Jacques Cousteau introduced us to surface waters. Now it's time to explore the deep. Manned exploration of space is science fiction. The adventure of the abyss is science fact.

Frank Pope is the Times ocean correspondent

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