Tuesday, February 3, 2009

Origins 9, First Cells

The three domains of life are divided into Bacteria, Archaea and Eukaryotes. Every organism has a set of genes which is used as a pattern for building the organism itself and passing along the pattern to the organism's offspring. The collection of genes in an animal is called the genome. Scientists have been able to do what is called full-genome sequencing, determining the entire make-up of these genes within individual organisms, since 1995. The genes are made of DNA or RNA, molecules made up of atoms in specific orders. On Oct. 23, 2008, an article which compares Bacteria and Archaea, which are mostly one-celled organisms, was published in the journal, Nucleic Acids Research, 36:21, pp 6688-6719. It is called, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," written by Koonin and Wolf. (A link to the entire free PDF article is found at the right on this abstract link).

Though only a small percentage of species have been sequenced, the introduction to the article explains that the researchers feel the work done so far is representative enough to survey patterns. One of the purposes of whole-genome sequencing is to compare the make-up of the genes and see if the orders of the molecules matched what scientists expected according to evolution theory (including the order in which organisms may have appeared on Earth).

Perhaps you have heard already, in the news or elsewhere, that the pattern of organism genomes has not produced a "tree of life" as Darwin predicted. At first, the term "web of life" was used as a substitute to tree. But now, Eugene Koonin, one of the authors of this article, asserts that web is even too clear a term for the genetic patterns. If you look up the article, you can see a picture on page 6708 which represents the new dynamic view of the genetic pattern for life. It is a group of circles representing genomes with lines connecting them every which way.

One of the reasons for this lack of clear, Darwinian progress is believed to be "Horizontal Gene Transfer" or HGT . Bacteria and Archaea are able to switch genes from one adult to the another by a few different mechanisms. Therefore, the patterns of adult to offspring are not closed or caused by internal mutation. Genes (part of the genome which is productive in protein make-up) are present when they shouldn't be and not present when they should be, according to what is expected. Many genes are found only in one or two organisms, never to be seen again. Considering the complex protein products they make, the sudden appearance and disappearance does not sound like slow, random change predicted by Charles Darwin.

There are limits to HGT and how much it can explain. The closer the organisms are in type and location of growth, the closer the genes to each other. Also, we are talking here of one-celled organisms. Multi-celled would not be so easily affected by HGT. The article states that HGT is still controversial, unable to explain all the differences. And, most obvious, there have to be genes in the first place in order for them to be exchanged. I had talked about LUCA, the last common unknown organism, in a previous post. Because the Archaea and Bacteria cells are so different, there would have had to be a great variety of genes in a single organism that existed previously that can be figured to be the original organism. The computer program came up with a cell with at least 1000 different genes, probably much more. Koonin, in the article mentioned above, interesting points out on page 6701 that a free-living cell would need a minimum of about 1000 genes.

Genes are an average length of 1000 nucleotides. A free-living cell would need at the very least about one million nucleotides of DNA in specific, functioning order to survive well enough to reproduce. Though not all those would have to be in one exact order, a large percentage would have to be in specific sequence to make functional proteins. As you might guess, this is far beyond what we would expect from the random movements of atoms, which themselves follow certain laws of chemistry.

That leads us to next post, where we will take a look at smaller organisms than cells--the viruses--and see if their genome patterns lead us to any knowledge of how life began.

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