Tuesday, October 6, 2009

Unintelligent Design (Part II)

I promised I'd tell you about the unintelligence of RNA transcription, so here it is. To understand just how stupid our cells are about this, we must again contrast our process with that of bacteria.

Most organisms store the bulk of their genome in DNA. The double helix is more stable than the single helix of RNA. 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 non-coding DNA interspersed between, and sometimes within, the recipes. Some of this is used in telling your cells when to make various recipes. Some of it is bits and pieces of genes that viruses have inserted into our chromosomes - enemy recipes that can sabotage your kitchen. Some of it is pieces of our own recipes that are accidentally duplicated when new copies of the cookbook are made. Eukaryotes like mammals, bugs and trees also have spans of non-coding DNA within their 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 have to copy it first. That's fine with the cells, because the machinery that uses the recipes can only take RNA anyway. That's the job of an enzyme called 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 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 begining of the genes that basically say, "start here." 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 on 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 what it looks like: 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, copies the important information, and ends at the end signal. We organisms with nuclei have defective polymerases that no longer recognize the ends 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?

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