individuals that reads: ATTGC in Harry, AATCA in Jim, GATGC in Betty and ACTGC in Bertha. A plausible sequence that might have belonged to their last common ancestor (the proto-Harry-Jim-Betty-Bertha) would be AATGC, since only one base change is needed to change the ancestor sequence into any of its modern descendants. Harry, Jim, Betty and Bertha could be said to belong to a gene family. If the DNA of another individual, Ted, was sequenced as AATTT we then could conclude that Ted was more distantly related to Harry, Jim, Betty and Bertha since two sequences changes are required to connect his sequence to any of the others. The last common ancestor of all five individuals, the proto-Harry-Jim-Betty-Bertha-Ted must have lived earlier than proto-Harry-Jim-Betty-Bertha. Just as with words, DNA sequences can be used to draw up family trees, only this time the tree reflects genetic rather than cultural inheritance.
Carl Woese of the University of Illinois was the first to make extensive use of DNA sequences to examine the early evolution of living creatures. He used the gene sequences encoding one of the sub-units of the ribosomes (the protein-making machine in cells) as a gene clock to construct a universal genetic tree. The tree divides all life into three domains. The first contains the eukaryotes (whose DNA is enclosed within the nucleus) which includes the unicellular protozoa (such as amoeba) and multicellular plants, fungi and animals – and us. The other two domains both consist entirely of prokaryotic (which means before the nucleus – whose DNA is not enclosed within nuclei) organisms. The eubacterial (true bacteria) domain contains most of the bacteria we are familiar with, such as E. coli. The third domain is that of a newly recognized bacterial group, called the Archaea.
Many aspects of the tree agreed more or less with evolutionary thinking. The ribosomal RNA sequences of the multicellular animals’ groups (vertebrates, worms, sponges, arthropods etc.) diverged at roughly the time of the Cambrian explosion. The rRNA of plant chloroplasts (which have their own DNA including rRNA genes) was found to be similar to bacterial rRNA, tying in with a theory championed by Lynn Margolis in the late 1960s, that these organelles were descended from symbiotic bacteria. The separate deep branching of eukaryotic (animals and plants) genes did come as something of a surprise. Until then it was generally assumed that eukaryotes had branched off from some bacterial ancestor billions of years ago; but that would have left us closely related to one of the bacterial groups. There was no evidence for this in the tree. Eukaryotes appeared as ancient as bacteria. This feature of the universal tree still remains a puzzle.
The recognition of the Archaea as a distinct domain of life also came as a major surprise to biologists. We have already met some of the Archaea in Chapter Two. The extreme thermophilic bacteria thriving in the undersea vents; the halophiles living in briny waters; and the methane-producing bacteria, are all Archaea. They have markedly different enzymes, fats, and cell structure to eubacteria and eukaryotes. Scientists had until then considered them as bacterial oddities but Woese’s analysis placed them as a separate form of life that, at a molecular level, is quite as different from, say, E. coli as we are. Scientists have sequenced all 1,664,976 DNA bases that make up the genome of an Archaea called Methanococcus janaschii, fished out of a two thousand, six hundred metre deep ‘white smoker’ hydrothermal vent chimney. Many of its genes are similar to those found in eukaryotes, suggesting that our nuclear genome may be the descendant of an ancient archaeon.
HOW DID GENES EVOLVE?
By and large, gene sequence data supports the neoDarwinian notion that gene evolution has involved a series of gradual modifications of existing genes through mutations. Nevertheless, problem areas remain. The first (already mentioned): how to account for apparent big jumps. A related problem, apparent in the DNA record, is the relationship between the major protein families. Examination of genes from diverse organisms has established that all modern proteins fall into about a thousand distinct protein families’. Although evolution within protein families, such as the globin (the protein in haemoglobin) gene family, can generally be traced through a number of antecedent proteins present in living creatures, finding the links between the protein families is much more difficult. Animal globins bear some relation to oxygen storage proteins found in bacteria but there is little or no identifiable relationship between these globin-related proteins and any of the nine hundred and ninety-nine or so, other protein families. The same is true for all the other protein families – there is much evidence for Darwinian evolution within the family, but no obvious close relative from which the family could have evolved. Each protein family is like a separate galaxy (of related proteins) in a vast outer space of protein sequences. New protein families must have arisen from existing proteins by some kind of mutational process but how their sequence traversed this vast empty sequence space devoid of Darwinian intermediates, is a mystery. It seems molecular evolution often proceeds though a series of small steps but that sometimes it takes big leaps – rather like the punctuated evolution envisaged by Gould and Eldridge. Big leaps are big problems for neoDarwinian evolution because the chances of a big jump landing anywhere useful are generally thought exceedingly small. As Richard Dawkins states, ‘However many ways there are of being alive, it is certain that there are vastly more ways of being dead …’3
Another problem for the neoDarwinian process is the evolution of metabolic pathways. This is a kind of molecular version of the eye problem – how to evolve complex structures – but its solution is not as apparent as the evolutionary pathway that led to the eye. The basic problem is that the complexity of biochemical pathways (unlike the eye) do not appear reducible. For instance, one of the cell’s essential biochemicals is AMP (adenosine monophosphate) the precursor of ATP (the energy-carrying molecule) which also finds its way into DNA, RNA and many other cellular components. AMP is made from ribose-5-phosphate, but the transformation involves thirteen independent steps involving twelve different enzymes (which we will represent as: A→B→C→D→E→F→G→H→I→J→K→L→M where A is ribose 5-phosphate and M is AMP). Each of the twelve enzymes involved in this pathway is absolutely essential for the biosynthesis of AMP. Darwinian evolution would require this complex system to have evolved from something simpler. But, unlike the eye, we cannot find the relics of simpler systems in any living creatures. As far as we know, nothing simpler works. Half or a quarter or a twelfth of the pathway does not generate any AMP or indeed anything else of value to the cell. It appears that the entire sequence of enzymes is needed to make any AMP. But without viable stepping stones, how can the entire complex system have evolved through Darwinian natural selection?
One explanation often cited is that complex biochemical pathways have evolved backwards. The story goes that the primitive cell initially utilized the final biochemical in the pathway (M or AMP) directly, as it was already available in the primordial soup. However, as primitive cells used up the supplies of M, any cell that evolved the capability of making M from another available biochemical would have had a selective advantage. One of those biochemicals was L, and a cellular innovator soon evolved an enzyme which could perform the transformation of L → M. Eventually supplies of L were, in their turn, depleted, creating selective pressure for a second evolutionary step to acquire the enzymatic capacity to make more L from one more readily available biochemical, K. Eventually, the entire pathway: A → B → C → D → E → F → G → H → I → J → K → L → M, evolved through this series of backward steps.
The problem with this explanation is that it requires all of the intermediate biochemicals (B,C,D,E,F,G,H,I,J,K,L) to have been sloshing about in the environment of the primitive cell. Yet AMP is a ribose sugar, that goes into making RNA. We will soon be exploring the enormous difficulties in making ribose sugars by the kind of inorganic chemical processes going on within the early Earth. As you will see, it is unlikely that even one, never mind all eleven, of the biochemicals in the pathway from ribose 5-phosphate to AMP was present in any significant quantity in the environment of the primitive cell.
In his book Darwin’s Black Box, the biochemist Michael J Bethe of Lehigh University considered
