Morton makes some interesting challenges to the flood-based interpretation framework of earth history, but nothing that seems to me to be a knock-out punch.

He makes several errors in this paper which would skew his results.

For example, some of his calculations are based on a year-long flood. As most Bible-based flood adherents would admit, Noah and his family and the animals were indeed in the confines of the ark for about a year (c. 375 days). But it's obvious that a flood is not over when the flood victims step from the rescue boats, but rather when the flood waters recede back to their former level, or to a new state of equilibrium. It might be argued that we're still not to equilibrium, but at any rate, few would doubt that the flood "continued" for some time after Noah left the ark. Many flood geologists would attribute the "Ice Age" to the repercussions of the flood, about 500 years later. They also would attribute the drying up of the Great Salt Lake Basin (Utah, USA), the carving out of the Grand Canyon (mostly Arizona, USA), and perhaps the filling up of the Mediterranean Basin to the after-effects of the flood, perhaps centuries later. When referring to the Haymond beds, which are 1300 meters thick, Morton claims that "[e]ven allowing for a daily cycle, [it] would require 41 years for this deposit to be laid down." With a flood lasting one year, he has indeed presented a show-stopper. With a flood lasting years, perhaps centuries in places, it's still a challenge, but not a show-stopper.

Morton's basic gist in this paper is that the Geologic Column does exist in entirety (essentially) in several places on the earth. Of course, that's not the question. The question is "How was this column deposited? Rapidly, over a short period of time, or slowly, over eons?" (And it's healthy to remember that rocks don't come out of the ground labeled "Devonian" or "Permian"; they are labeled by humans, viewing through their world-view glasses, who have interpreted these rocks to be Devonian or Permian.)

Morton also refers to burrow and shale deposition and mud cracks as evidence against the flood. The burrows and mud cracks are unconvincing to me (and have been addressed elsewhere (a quickly-Googled example at creationwiki[dot]org/Flood_geology#Fossil_Burrows)), but the shale deposition will require additional research.

No, I don't know of any one particular article that better defends the flood model; but there's enough questions about the mainstream view (polystrate fossils, anyone? bent, but not broken, rock strata? 122 meters of strata deposited rapidly at Mt. St. Helens, 7 of which were deposited in a single day (above reference), carving out of a 27 km-long canyon 42 meters deep in a single day (above ref.), submarine canyons larger than the Grand Canyon running thousands of kilometers into the oceans (above ref.), massive lava flows unlike anything we've ever observed under today's conditions, etc) that convince me that a person should really be open-minded about an alternative interpretive framework of earth history.