As an example, there actually is a "scientific" explanation for the splitting of the Yam Suf. The point is that a wind could have blown and uncovered a ridge of land across the sea. Hashem took this and changed it to be sufficient for the entire Bnei Yisrael as well as adding the miracles specified by the midrashim. It also kept the Egyptians away until they crossed as well as making the timing exact.
Scientists Explain Red Sea Parting and Other Miracles
In the latest attempt to lend scientific credence to a supernatural
event, Naum Volzinger, a senior researcher at St. Petersburg's
Institute of Oceanography, and Alexei Androsov, a colleague based in
Hamburg, Germany, analyzed conditions that could have made the parting
of the Red Sea possible.
As the biblical story goes: "And Moses stretched out his hand over the
sea; and the Lord caused the sea to go back by a strong east wind all
that night, and made the sea dry land, and the waters were divided."
Volzinger and Androsov calculated that a wind blowing at the speed of
67 miles per hour sustained overnight could have exposed a reef that
existed close below the ocean surface. The Israelites could have then
fled over the passage before the wind died down and waters rose again,
blocking the way for pursuing Egyptian soldiers in their wheeled
Volzinger explains that some 3,500 years ago, the reef would have been
closer to the water's surface so it would have been exposed for just
the right amount of time.
"It would take the Jews … four hours to cross the 7-kilometer reef
that runs from one coast to another," Volzinger told The Moscow Times.
"Then, in half an hour, the waters would come back."
A miracle? Perhaps. Great timing? Certainly, argues Colin Humphreys, a
physicist at Cambridge University in England and author of the book,
The Miracles of Exodus.
"I still say they're miracles," Humphreys said. "But I think the
miracle is in the timing."
There is a scientific explanation for the parting of the Red Sea in Exodus
Application of storm surge modeling to Moses' crossing of the Red Sea
Two case studies are presented. A reconstruction of the crossing of
the Red Sea by Moses and the Israelites, as described in Exodus 14,
shows that the eastern Nile delta of Egypt matches the Biblical
narrative and provides a hydrodynamic mechanism for water to remain on
both sides of the dry passage. The vulnerability of Manila Bay and the
surrounding areas to a Category 3 typhoon is evaluated and shows that
the simulated surge heights depend heavily on the wind direction and
the coastal topography.
Dynamics of Wind Setdown at Suez and the Eastern Nile Delta
Under a uniform 28 m/s easterly wind forcing in the reconstructed
model basin, the ocean model produces an area of exposed mud flats
where the river mouth opens into the lake. This land bridge is 3–4 km
long and 5 km wide, and it remains open for 4 hours. Model results
indicate that navigation in shallow-water harbors can be significantly
curtailed by wind setdown when strong winds blow offshore.