Unique Genes

A very important research paper was published in 2008 by researchers of the National Center for Biotechnology Information (NCBI). I already discussed it back in February (HERE) when I was writing a series about biological origins. It is by Eugene Koonin and Yuri Wolf, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36, 21 (Dec. 1, 2008): 6688-6719.

The paper reports on the gene make-ups of bacteria and archaea. Archaea are a group of organisms that were thought to be bacteria until the 1970's, but were found too different to group in the same category.

There are reasons this paper and the research it reflects is so important. As the researchers determine the specific gene sequences in more and more organisms, they are finding a pattern, but it is not neo-Darwinian. First, there is a small core of genes that appears almost unchanged in most of the organisms (what they call "highly conserved"). Second, there is a larger amount of genes that are "moderately common." And last but not least, is a huge amount of genes that appear in one or just a few organisms (are "narrowly distributed"). However, these statistics should not be confused with the gene make-up in a particular organism. There you will find the small core of common genes, a larger set of moderately common genes, and a smaller set of unique genes (the unique genes are a larger group of genes but a smaller percentage in each individual organism).

The graph above is from the article. It is called a self-organizing map or SOM. It shows the spaces between groups of genes, called COGs (Clusters of Orthologous Groups). The "Orthologous" in that name means "coming from a common ancestor." (As an aside, similar gene sequences are assumed here to be from common ancestors, although design advocates say they could be from common design.) The spaces between the isolated clusters shows that there is no progressive, Darwinian relationship between these organisms. They are all unique in certain ways. And the gene groups themselves each had to become functional on their own--they did not inherit them from other groups in a Darwinian way. This makes the origin of life much more difficult to support by neo-Darwinian theory.

The authors of the paper and many other scientists want to quickly claim that a new phenomenon, Horizontal (or Lateral) Gene Transfer, can explain these new findings. HGT is the transfer of genes between organisms. But they are wrong to suppose that HGT can handle the vastly improbable odds of the existence of all these unique functional genes any more than gene mutation could have. First of all, you have to have functional genes before they can be transferred. I have touched upon HGT HERE. As the information about biological life increases, I hope that more and more people realize the immensity of these discoveries.

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I am now finished, for at least a while, with Intelligent Design Theory. There are surely more things I could say, but I've covered a lot. If you are interested, please see my ID link in the right column and read the past posts. I am not an expert, although I have a bachelor's degree in animal science and have been able to learn a lot on my own. I feel I can introduce the subject to others, but at this point I don't have the inclination to delve into the advanced mathematics and chemistry of the subject. I don't want to spend all my time trying to master new fields of study like biological computing and genetic algorithms. I hope the next generation will enjoy the adventure of learning more and more about God's world.

And yet, as I move onto other things, I can't give up ID completely. The physiology of biological life is startling, and each time I look at a new "Molecule of the Month" at PDB-101, I am amazed. I have given many links in the blog so you can go and discover the fabulous world of biology.

We praise God through Jesus Christ for His awesome, beautiful Creation!

2013 Update: My interest in Intelligent Design Theory has changed to what is called "Special Creationism," the belief that God created species, including humans, separately and directly.

LUCA

Before the advent of gene sequencing, the theory of evolution was based on morphology (physical characteristics). Then, scientists developed methods to find the make-up of the gene. The gene is made of a set of 4 molecules which repeat, which we call nucleotides (Wikipedia entry HERE). They have names but are often nick-named A, T, C and G. These nucleotides combine in an order that acts as a code, which is read by other cell units and turned into proteins which do much of the work of the cell.

The National Center for Biotechnology Information (NCBI) is taking the sequences found by researchers all over the world and comparing them. Many of these sequences are done on small organisms of single cells. Bacteria were considered the only organisms to be of one type of cell, the prokaryote (pro-CARry-oat) type. In the 1970’s, scientists realized there was another type of prokaryote, called archaea (ar-KEY-ah). They were considered a separate domain from bacteria and a third one, eukaryotes (you-CARry-oat). The third type is the one in plants and animals, including humans. To make things more complicated, each of the domains have branches, so they need to find common ancestors to the branches for each of the 3.

Unfortunately for the advocates of Darwinian evolution, the results of the sequencing have shown anything but a clear-cut progression from an organism which can be considered the simplest to the next which is more complex and on up to human scale. I will talk more about that next week. But the point is important because it moves the search "back" to a previous ancestor that would have shared genes of all of them and been able to branch off into the 3 distinct domains we see now.

In a paper, Makarova et al., "Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea," Biology Direct 2, 33 (2007), they discuss the findings of comparitive gene studies (orthologous means genes that come from a supposed common ancestor). The conclusion for the archaeal branch is:

Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles.

They estimate it would have had to have at least 996 genes. As they say, it is almost as complex as modern organisms. And archaea are believed to have been present as long as 3.5-3.8 billion years ago. Where then does the common ancestor of all organisms fit? They are running out of back time for all the gene sequences to fall into place, because some scientists think the Earth was too hot for organisms to form until around 4 billion years ago.

Next time, for my last regular ID entry, I will talk about the NCBI results which show the end of genomic Darwinian evolution before it even begins.

2013 Update: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species, including humans, separately and directly. Much of the biological science in ID is similar to Special Creationism.

LUCA to come

I've been really busy this week, so I'll just give you an intro into my next Intelligent Design theme, which will be related to some in the past. Of course, biological life is all intertwined, but there are distinct categories we work with.

I've had a series about "Origins" which started HERE. I talked about some of the issues of naturalistic, materialistic theories for the beginning of life. One concept I mentioned was the "Last Unknown Common Ancestor," abbreviated LUCA (HERE). Though the term does not in itself indicate a very first organism, it heads in that direction. It includes research into what genes and proteins the ancestors of present-day species would have needed in order for the organisms of today to be what they are. It considers the number of possible offspring that a certain organism could have through the generations and how much the inner workings could have changed in that time (on a natural basis).

In fact, I've found some very interesting research on this, and hope to get into the details by next week.

2013 Update: My interest in Intelligent Design Theory (ID) has changed to what is called "Special Creationism," the belief that God created species, including humans, separately and directly. Much of the biological science in ID is similar to Special Creationism.