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DNA by the Numbers

DNA by the Numbers


An avid fan of spy stories, I have read many which involve an apparently harmless document (like a friendly letter). But the document actually conveys dangerous information if one is provided with the appropriate convention for decoding it.

That situation reminds me about the case of two creatures, one a human and the other a chimpanzee. Some scientists declare that the genetic material of these two organisms is 98% the same and this proves that the humans are descended from the chimpanzee. A closer look at the situation, however, reveals that this declaration actually means nothing.

The first question anyone reading about human and chimp relationships should ask is, what do those numbers mean? These numbers are computer estimated similarities in the content of DNA. That molecule consists of four choices (like letters) which provide the genetic information bearing part of a chemical chain. The choices are called A, T, C and G. We could potentially arrange these letters in many different patterns in a row (sequence) such as CATCATGAT or TTTACGGAC or whatever we choose. There are actually about 3 billion letters in the entire collection of human genetic information (genome) and even more in the chimpanzee genome.

By means of machines and chemical strategies, the order of the letters along the human genome has been quite well documented. Then in 2005, a description of the chimpanzee genome was published. This is said to be 98% similar to the human genome. In comparison, the rat’s genome is said to be 88% similar to the human genome, and chickens are estimated to be 60% similar. There are however many reasons why these values mean very little.

What scientists did was to chop up the chimp DNA into millions of small fragments about 500 to 1200 letters in length.  The order of letters on each piece was then documented. But how did they put the whole thing back together again? For a start, computers compare fragments from several machines, looking for pieces with overlapping order. The computer then connects adjacent parts into larger pieces of information called “sequencing contigs” meaning continguous [adjacent] pieces of information. Rather than continue this expensive process indefinitely however, the scientists also used the human genome as a template or standard pattern to arrange and connect fragments. This is like using the picture of a puzzle to figure out which pieces should go where.

The result of this process is that the chimp genome might inadvertently have been made to appear more similar to the human genome than it actually is. Indeed the only two sequences which have been comprehensively mapped in both chimpanzee and human are two tiny chromosomes: chromosome #21 and the male gender determining Y chromosome (Nature January 28/10 p. 537). While the chimp and human chromosome # 21 are indeed very similar, comparison of the Y chromosome has provided a big surprise. The male-specific region of the Y chromosome (MSY) in these two species reveals that “they differ radically in sequence structure and gene content.” (p. 537). The chimpanzee MSY exhibits 19 massive palindromes, compared to only 8 in humans. A palindrome is a sequence of letters which reads the same in both directions such as “Madam, I’m Adam.” Comparison of the two sequences shows great differences in information content and arrangement of the information. Apparently scientists did not expect and cannot account for these marked differences (p. 538).

Scientists had approached the comparison of genetic code in various organisms such as human and chimps, with high hopes that the identified differences would explain the contrasting characteristics of these organisms and how they got that way. Unfortunately these hopes have proved entirely unfounded. Indeed these people had assumed that it would be possible, through comparison of DNA from various organisms, to track the process of increasing differences from a common ancestor to more remote descendants.  What actually happened however was: “When the genomes started coming out, a lot of people thought they could track the regulatory code just by comparing sequences … that would have been really nice, but unfortunately it doesn’t work. You do find patterns, but they’re not necessarily relevant.” (Nature Nov. 8/07 p. 142)

Scientists still cannot explain what there is in the genome that provides for our special characteristics, or what makes us human. (Nature Sept. 1/05 p. 51, 83) They now know that variation in the ordering of the letters in the DNA is not enough to explain the differences between humans and chimps.

For many years scientists anticipated that differences in genes would give clues about lines of evolutionary descent. The idea was that if both groups are descended from the same ancestor, then both groups initially started out with the same genome. However with increasing time, greater differences should appear between the two groups. Nevertheless as more genomes were studied, surprises began to appear. Apparently even very different organisms may exhibit similar genes. Thus one commentator pointed out: “Many of the genes that determine the animal body plan are virtually identical in both structure and function in creatures that, on the outside, have little in common.” (Nature Nov. 20/08 p. 300) Similar genes then are not necessarily an indication of any kind of close relationship. Indeed similar pieces of information may do different things in different organisms. Thus “it is clear that all things are not equal: the function of any given gene cannot be defined outside its species specific context.” (p. 303)

The main problem with using DNA to explain the characteristics of organisms however is that scientists now realize that we do not even know what a gene is. Genetic information was formerly imagined to consist of strings of genes, each one controlling one characteristic. There was also ample filler material, formerly called ‘junk DNA’ but now known to be important in control and regulation of genetic expression. The problem scientists have now discovered is that identical strings of DNA can in fact be read in totally different ways (like the spy’s letter). One commentator pointed out the result of this situation: “As long as we remain unsure what a gene is, we are a long way from understanding genomic evolution.” (Nature Feb. 14/08 p. 772).

The image scientists had developed of genetic information has now dissolved into “mind-boggling complexity.” (Nature May 25/06 p. 399) Whereas formerly genes were considered to be pieces of information strung end to end like beads on a string, it now appears that there are no individual pieces of information. Rather, the cell copies a piece of information, snips out some parts and attaches the remaining pieces together in various orders and numbers of pieces. Thus one stretch of DNA, depending upon which fragments are joined together and in what order, can yield endless different proteins, all from one piece of code. Moreover it appears that these transcripts often overlap with each other. There have been cases found of one protein coding transcript nestled within the non-protein coding discarded section of another transcript/gene and of one protein coding transcript formed by combining component parts that are located far distant from each other on the chromosome with several other ‘genes’ in between. (p. 399-400) Thus as the author of the article declares: “Discrete genes are starting to vanish. We have a continuum of transcripts.” (p. 400) Obviously it is pointless to compare the genomes of organisms when these tell us so little about the organisms involved.

It is apparent then that scientists are not in a position to compare human and chimpanzee genomes Even if the genomes were identical, it would give no clues about relationships because of the alternative splicing of genetic information and multiple reading frames from the same piece of stored code. Moreover the actual form and function of creatures appears to come from higher levels of control about which we know very little. Thus assumptions that similar genomes suggest a close evolutionary relationship, are plainly without any kind of logical basis. All that scientists have discovered is how little we understand.

The study of various genomes obviously has been a story of secular disappointment. What is called for here is humble appreciation of what God has told us concerning how He created all things. Then we interpret the data from nature in terms of what God has revealed in His Word.

Margaret Helder
November 2010

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