In an advanced alien civilization which has passed through the genetic grand transformation, when all biological, neurological and psychological research is completed and accurate and consistent theories are available for everything in those fields, and in addition, all the data available about living organisms is known, there would be extensive use of this knowledge. We cannot, from the current state of our ignorance, predict there will be this or that usage, but it seems highly probable that there will be some industrial uses of genetics. Today we have some of this, and as a matter of fact, we have had such factories ever since fermenting was discovered.
Cheese, risen bread, beer and wine, along with other fermented vegetables, fish, and some other products, are produced by the use of microorganisms here on Earth. These products represent the simplest possible biofactories, but there is no reason whatsoever to think they are the only ones which will be economically efficient once genetics becomes understood. Even if an alien world did not have yeasts which cause bread to rise, the existence of extensive genetic knowledge would allow such a microorganism to be invented, and then the alien civilization would have risen bread, if they wanted it.
These products involve using whole cells, in an agglomeration, to produce chemical changes in other foodstuffs, producing carbon dioxide, alcohol and lactic acid. There is a natural inefficiency in using whole cells for this, as the cell walls slow down the throughput of the chemicals used for input and output by the microbes. If there was a way to have this reaction without cell walls, the biological factories could be more dense, and possibly more efficient and better controlled. Thus, in an advanced alien civilization, we might see biological factories, producing a great many useful materials, without cells. Instead, a vat would serve as a giant cell wall, while the contents were chosen as only those minimally necessary for the biochemical production.
This advance, assuming it is possible, seems to tear down the wall between biology and organic chemistry. Inside the vat there might be no mitochondria, but instead industrially produced ATP was added as fuel for the reaction. Then the proteins that microbes normally use to catalyze and power the transition would consume the ATP fuel and create the right output. Inside a typical cell there are thousands of proteins with different functions, and only those few necessary to synthesize the desired product would be necessary. If the output molecules were smaller than the proteins needed to make them, a filter would be all that was necessary to extract the output. Likewise, input chemicals might be small enough to pass through a filter which blocked the factory proteins.
The pre-genetics method of making medium weight complex organic molecules can be quite tedious using solely the methods of organic chemistry. A tailored genetic process could be more efficient and more productive, based on resource and energy consumption.
As part of the genetics revolution, the biochemistry of nutritional needs will surely be understood. Once that is done, agriculture might be relegated to specialty production, and the majority of food production will take place on these biological factories. There could be no need for sunlight for these factories, although certainly some development of chloroplast-like nodules might happen and vats could be provided with energy in the form of photons, rather than by fuel in the form of ATP. If this happens, food would be produced by combining nutritional inputs produced separately, and an entirely new food industry would be born. There would be no need for the biofactories to be located outside the arcologies, or wherever the aliens chose to live, but they could be positioned nearby residential areas, to minimize transportation costs and delays.
If agriculture is slated to disappear after the genetics grand transformation, this means that a huge telescope, large enough to image distant exo-planets, would not see huge parts of the dry land of an exo-planet with an advanced alien civilization turned over to monocropping. In fact, there might be very little visible from agricultural uses, as specialty crops could also be produced in biofactories as well. Freshness is not an issue if the fruit or vegetable is grown a kilometer from your residence.
As noted elsewhere, advanced methods of resource usage reduction will be used to prolong the time that the civilization can depend on buried resources. Recycling of resources would be used as well, so there might not be huge quarries that could be visible from space. Energy supplies, whether that would be uranium and thorium or low atomic weight fusion ingredients, would also be preserved by minimizing the losses of energy, such as for heating residential and industrial areas. Insulation would have been perfected. This implies that there would be no giant infrared signature from the arcologies.
In short, three of the main observational items that we on Earth, in later centuries, might have thought to use to detect alien civilizations with a giant space-based telescope would very well not exist. The biggest detectable would have been agriculture, but that disappears with the genetic revolution. Mining sites, such as huge open-air quarries formed by scraping off the top layer of dirt to gain access to shallow buried resources, would not necessarily still be in use. An example of these would be the tar sands region in Canada. Lastly, the habitations themselves would not be emitting light or infrared in massive amounts, such as our Earth cities do today, instead, there would be only minimal energy being spread out and leaking upwards towards space.
Finding something to search for is quite a challenge. Recall that there are only a few millennia between the emergence of the civilization from the primitive hunter-gatherer level up to the asymptotic technology level, and it would be incredibly coincidental if we happened to turn our telescopes on during that interval. If an advanced alien civilization can last a million years, order of magnitude, it is totally likely that we would observe their planet after they had made all the changes needed to last that long, including agriculture replacement, recycling and waste reduction, and resource use minimization. They would essentially be hiding in plain sight.
