More Unintelligent Design

Both eukaryotes and bacteria must transcribe the genes in their DNA into RNA transcripts in order to use them. The process starts out much the same in both kinds of organisms. In bacteria, the process is logical and efficient. In eukaryotic organisms like plants, fungi and animals (us), the process has gone hideously awry, and evolution has again employed a sloppy and inefficient fix.

Most organisms store the bulk of their genome in DNA. The DNA double helix is more stable than the RNA single helix. DNA is a long list of genes, you can think of them as recipes in a cookbook. (It isn't set up like a logical cookbook. There are long spans of gobbledygook between the genes, which have to be edited out each time the gene is used.) DNA is the master copy of the cookbook. It's stored in the nucleus, away from all the ingredients, so the pages don't get torn, singed or spilled upon. In order to make the recipe, you must first make an RNA copy that you can take out of the nucleus, but you had to make the RNA copy anyway, because the machinery that uses the recipes can only read RNA. We call the enzyme that makes the RNA copy from the DNA polymerase. In eukaryotes, the polymerase transcribes the gene into RNA in the nucleus, and the RNA is taken out of the nucleus to be put to further use. Bacteria have don't have nuclei, but they still have to make the RNA copy of the gene in order for their machinery to put it to use.

Both bacteria and eukaryotes have promoters - sequences at the beginning of the genes that signal where the copy should start. Bacteria and eukaryotes also have sequences that signal the end of the gene, but they work differently. In bacteria the "end" signal is called a terminator. When the polymerase reads the terminator, it detaches from the DNA and releases the RNA copy to be used by the cell. Makes sense.

When eukaryote polymerase gets to the "end" signal, it transcribes it and keeps going. The transcribed end signal causes proteins that have been monitoring RNA transcript to cut off the transcript and take it away for processing so it can be used by the cell. Meanwhile, polymerase keeps going like a runaway train, transcribing hundreds of nucleotides, whatever happens to follow the gene. Biologists haven't completely figured out what happens next, but here's their best guess: An enzyme comes up and digests the trail of RNA gobbledygook that the polymerase is spewing out, recycling it back into unattached nucleotides. When that enzyme reaches polymerase, it knocks polymerase off the DNA, and transcription stops.

To summarize, bacteria have a system that works perfectly. Their polymerase starts at the start signal, transcribes, and stops at the stop signal. We organisms with nuclei have defective polymerases that no longer recognize the stop signals. Rather than fix the polymerases, evolution threw us some proteins to collect the RNA transcript and then another enzyme to clean up the mess and slide tackle the runaway enzyme off the DNA. That deserves a very special contraction: untelligent design. Keep in mind that every time polymerase attaches a nucleotide to the RNA strand, it's using energy - the equivalent to one ATP molecule. We don't get that energy back when we recycle the nucleotides. What kind of Intelligent Designer would have left such a mess?

Then again maybe there is some wisdom here. Bacteria are better at both DNA replication and RNA transcription. Maybe the Designer made the universe for the bacteria, and we're just here to be their hosts. After all, for every human cell in your body, you also have ten to twenty bacteria living in and on you - in a magnificent diversity of 500 - 1,000 different species. That's about 10¹², or 1 million × 1 million, bacteria living in and on each and every one of us. All hail our glorious Bacterial Creator?