DNA by the Numbers
Comparing the Human and Chimp Genome
Have you heard the wartime story about Great Aunt Gertrude's letter? In the letter she talked on and on about her pet rabbits which insisted on multiplying so irresponsibly. She also discussed her difficulties with the laundry when the whites became stained with soot from the air. Though she was older, her health was quite good, so there was little in the letter on that score.
Two people ended up reading her letter. The first person took the letter at face value and thought nothing of it. The second used a complicated convention to extract a message about railroads and explosives. The text was 100 per cent the same in both cases, but the message extracted was entirely different.
That reminds me about the case of two creatures, one a human and the other a chimpanzee. Scientists have declared that the genetic material of these two organisms is 98 per cent the same, and that this proves humans and chimpanzees are related, descending from a common ancestor.
A closer look at the situation, however, reveals that this declaration is extremely simplistic and actually means nothing.
The first question anyone reading about human and chimp relationships should ask is, what do those numbers mean? When they talk about percentage similarities in genetic material, scientists are discussing computer estimated similarities in the content of the DNA.
That molecule consists of four choices of components (like letters) which provide the information bearing part of 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.
How they got to 98
By means of various 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 per cent similar to the human genome. In comparison, the rat's genome is said to be 88 per cent similar to the human genome, and chickens are estimated to be 60 per cent similar. There are however many reasons why these values mean very little.
Scientists did not spend as much money figuring out the order of the letters for the chimpanzee genome as for the human genome. What they did was to chop up the DNA into millions of small fragments about 500 to 1,200 letters in length. Machines then figured out the order of letters in these fragments.
But where should these be located in relation to the whole three billion or so letters in the entire collection? For a start, computers look for pieces of overlapping order when fragments from several machines are compared. In this way, the computer connects adjacent parts of the puzzle into larger pieces of information which they call "sequencing contigs" meaning contiguous (adjacent) pieces of information. However, rather than continue this expensive process indefinitely to build up the system, the scientists used the human genome as a template, or standard pattern, to arrange and connect pieces of information. 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 have inadvertently been made to appear more similar to the human genomes 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).
A closer look reveals big differences
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." In addition, more than 30 per cent of the chimpanzee MSY sequence has no similar counterpart in the human and vice versa. Comparison of the two sequences shows great differences in information content and arrangement of the information. Furthermore, the human MSY content exhibits one third more distinctive gene sequences and kinds of gene than its chimp counterpart. Apparently scientists did not expect and cannot account for these marked differences (p. 538).
Our differences can't be accounted for by our DNA
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 gnomes 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. Thus an article on Darwin's 150th birthday declared:
"(One man) was part of a group that pushed hard to sequence the genomes of human's closest relative, the chimpanzee, arguing that any genetic differences between human and chimp sequences would lead straight to the heart of humanness. But the chimp sequence, published more than three years ago, hasn't delivered this … the protein-coding sequences for genes expressed in the brain have changed very little across the species."
Nature Feb. 12/09 p. 776
For many years scientists focused their attention on genes, locations in the chromosome which appeared to control specific traits. It was 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 genomes. However with increasing time, greater differences should appear between the two groups. Nevertheless as more gnomes 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 that same article declared that what a given gene does, depends very much upon the creature that possesses it. 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).
We know less than we thought
The main problem with using DNA to explain the characteristics of organisms is that scientists now realize that we do not even know what a gene is. Genetic information was fairly recently imagined to consist of strings of genes, each one controlling one trait or 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 Great Aunt Gertrude'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 gnomic evolution.
Nature Feb. 14/08 p. 772
The nice neat 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 (formerly a gene) overlap with each other so that there are no distinct anythings. 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). It is evident in this case that it is pointless to compare the genomes of organisms when these tell us so little about the organisms involved.
Our information is hidden higher than in our DNA
There are yet other complicating features too, but one of these seems particularly relevant to this discussion. Some scientists have now come to the conclusion that we could compare the information content in the DNA forever but it will never tell us anything about why creatures are the way they are. That is because the information the scientists seek is perhaps controlled by some higher level of organization which scientists have yet to discover.
One commentator described the situation thus:
The information that determines biological function lies at a higher, more abstract level, in the entire network of genes, proteins and other factors that each act on the others in a series of nonlinear feedback loops. The body plan or feature that results is what scientists who study complex systems call an 'emergent property’ – one that is more than the sum of its parts.
Nature Nov. 20/08 p. 301
The article admits that it seems very improbable that such complex systems could develop spontaneously, as in an evolutionary process.
It is apparent then that scientists do not know how similar the human and chimpanzee genomes (total DNA content) really are because they have not carried out a complete unbiased study of the chimp genome. Moreover the apparent small differences between human and chimp genomes do not explain the marked differences between the two groups. 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 nothing. Thus assumptions that similar gnomes indicate/suggest a close evolutionary relationship, are plainly without any kind of logical basis. All that scientists have discovered is how little we understand.
There are other more technical arguments which supposedly prove that humans have descended from a chimp-like common ancestor. Based on the idea that humans descended from such an ancestor, similarities or differences between the DNA of the two groups are used to "prove" that this event in fact occurred. The popular arguments involve the vitamin C pseudo gene, human chromosome #2 and the pattern of ERVs (endogenous retroviruses). In every case there are good arguments against these conclusions.
In any case the secular scientist assumes that humans have, in fact, developed from animal ancestors. These scientists then look for patterns of similarity between humans and primates. These similarities are then taken as proof that such descent in fact occurred (a circular argument). However Christians are not bound by secular assumptions. They are free to consider that God, in His wisdom, could and did confer, at His discretion, characteristics similar or different to other creatures. In the case of separate creation of the animal kinds, such patterns tell us only about the Creator's wisdom in His choices.
The study of various gnomes obviously has been a story of secular disappointment. Not only were their hopes for enlightenment into evolutionary processes not fulfilled, but the major discovery is how complicated everything is and how little we understand. 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.