Limits on Evolution

Summary of problems:

Explore Evolution never defines "biological information," except through error-laden analogies to computers. Biologists have no trouble showing how new information (in the sense used by information theorists) originates, nor how new genes, kinds of cells or tissues evolve.

Full discussion:

Nowhere in the discussion of "the information problem" is there any attempt to formally define how students should measure "information." At one point, the authors introduce a strained analogy between upgrading computer software and adding biological information, but never quite explain the analogy. Later they observe that scientists have occasionally referred to DNA as if it were analogous to a computer program. Based on this informal analogical reasoning, they declare "So, biological information is stored in DNA" (p. 94). Teachers who wish to actually discuss this idea in class would be stranded utterly not only by Explore Evolution's treatment of the subject, but by the equally vague attempts by the ID creationists on whose work this section draws.

The field of mathematics known as information theory was developed to address the transmission of information, and it both defines information and describes how information is created. In essence, a mathematically random sequence of symbols (whether letters, DNA bases, or computer bits) has the highest information content possible. A completely predictable sequence contains only as much information as it would otherwise take to accurately predict the sequence. Thus, in information theory, adding random noise actually increases the amount of information being transmitted. Whether that information is useful or not to a listener is a separate matter.

This is where the misuse of "information" throughout Explore Evolution can be confusing. We usually have a very specific expectation for information transmitted over a telephone line, so random static on the line reduces the amount of information we can use. Randomness adds mathematical information, but decreases immediately usable information. A process of selection, mutation, and drift acting on such random information will, in time, extract new elements which are usable.

Evolution itself has no expectations about what data will be transmitted from generation to generation. Random mutations add information to the genome, and natural selection (or artificial selection) acts against those mutations which are not useful at a given moment, promotes those mutations which happen to benefit the organisms possessing them, and has no particular effect on mutations which do not influence the organism's fitness.

Biologists have incorporated this insight into their studies of the evolution of new genes. Gene duplication are common events, resulting from small errors in the process of cell replication. Once a gene is duplicated it is possible for one copy to mutate, adding information without risking the functioning of the pre-existing gene.

The process of gene duplication has been known since at least 1936; its possible significance for producing the raw material for the evolution of genetic novelty was recognized as early as 1951 (see Zhang 2003 for more on this history).

Examples of New Genes of Known Age (from Long, 2003), table 2)
Genes Age Evolutionary feature
Drosophila
jingwei 2.5 my A standard chimeric structure with rapid sequence evolution
Sdic <3 my Rapid structural evolution for a specific function in sperm tails
sphinx <3 my A non-coding RNA gene that rapidly evolved new splice sites and sequence
Cid Function diverged in the past 3 my Co-evolved with centromeres under positive Darwinian selection
Dntf-2r 3-12 my Origin of new late testis promoter for its male-specific functions.
Adh-Finnegan 30 my Recruited a peptide from an unknown source and evolved at a faster rate than its parent gene
Primates
FOXP2 100,000 y A selective sweep in this gene, which has language and speech function, took place recently
RNASE1B 4 my Positive selection detected, which corresponds with new biological traits in leaf-eating monkeys
PMCHL2 5 my Expression is specifically and differentially regulated in testis
PMCHL1 20 my A new exon-intron in the 3' coding region created de novo and an intron-containing gene structure created by retroposition
Morpheus 12-25 Strong positive selection in human-chimpanzee lineages
TRE2 21-33 my A hominoid-specific chimeric gene with testis=specific expression
FUT3/FUT6 35 my New regulatory untranslated exons created de novo in new gene copies; the family has been shaped by exon shuffling, transposation, point mutations and duplications
CGß 34-50 my One of two subunits of placentally expressed hormone; the rich biological data clearly detail its function
BC200 35-55 my A non-coding RNA gene that is expressed in nerve cells.
Rodents
4.5Si RNA 25-55 my A non-coding RNA gene that is expressed ubiquitously
BC1 RNA 60-110 my A neural RNA that originated from an unusual source: tRNA
Fish
Arctic AFGP 2.5 my Convergent evolution; antifreeze protein created from an unexpected source driven by the freezing environment
Antarctic AFGP 5-14 my Convergent evolution; antifreeze protein created from an unexpected source driven by the freezing environment
Plants
Sanguinaria rps1 <45 my A chimeric gene structure created by lateral gene transfer
Cytochrome c1 110 my Origin of mitochondrial-targeting function by exon shuffling
Protozoa
N-acetylenuraminate lyase << 15 my A laterally transferred gene from proteobacteria that recruited a signal peptide

As it has become more practical to trace the sequences of genes in multiple species, scientists have been able to identify genes which went through these processes, acquiring new functions within relatively recent history. That research systematically refutes the claim in Explore Evolution that "whether you're talking about artificial selection or about microevolution that occurs naturally, changes in the sub-population take place as genetic information is lost to that population" (p. 95). In fact, a recent review of the processes by which new genes and new gene functions evolved drew the exact opposite conclusion:

The origination of new genes was previously thought to be a rare event at the level of the genome. This is understandable because, for example, only 1% of human genes have no similarity with the genes of other animals, and only 0.4% of mouse genes have no human homologues, although it is unclear whether these orphan genes are new arrivals, old survivors or genes that lost their identity with homologues in other organisms. However, it does not take many sequence changes to evolve a new function. For example, with only 3% sequence changes from its paralogues, RNASE1B has developed a new optimal pH that is essential for the newly evolved digestive function in the leaf-eating monkey. Although it will take a systematic effort to pinpoint the rate at which new genes evolve, there is increasing evidence from Drosophila and mammalian systems that new genes might not be rare. Patthy compiled 250 metazoan [multicellular animal] modular protein families that were probably created by exon shuffling. Todd et al. investigated 31 diverse structural enzyme superfamilies for which structural data were available, and found that almost all have functional diversity among their members that is generated by domain shuffling as well as sequence changes.
Manyuan Long, Esther Betrán, Kevin Thornton and Wen Wang (2003) "The Origin of New Genes: Glimpses from the Young and Old," Nature Reviews: Genetics, 4:865

The table at the right describes a few well-studied examples of recently evolved genes, and a summary of what scientists have learned about the processes by which those genes evolved. The processes are the same sorts of small-scale mutational changes that we observe in existing populations. It was not necessary to invoke previously undescribed processes, merely to understand how known processes could produce the patterns observed in nature. That is the way scientists typically work, and an inquiry-based textbook ought to teach students to apply those methods. Instead, Explore Evolution ignores actual knowledge, criticizes the scientists who produced that knowledge, and discourages scientific inquiry from students, in favor of vague and untestable speculation.

Biologists do not dispute that limits to evolution may exist, and conduct research to test whether such limits exist. For instance, biologists wonder why no marsupials evolved flight or the sorts of adaptations to swimming seen in other mammals. It is hypothesized that the young marsupials' early crawl to the teat (see our discussion of marsupial reproduction in chapter 12) may place a constraint on the possible final forms the marsupial shoulder can take. While placental mammals give birth to offspring that are self-sufficient, marsupials give birth before major nerves, muscles and bones have formed, and must crawl to the teat (an exception is found in bandicoots of the genus Isoodon, which have a backwards-facing pouch into which the newborn can drop or slither without using its arms). That crawl requires that a functional shoulder exist early in fetal development, and the necessity of forming that functional shoulder so early may prevent the sort of limb diversification seen in other mammals, which range from the bat's wing to the cat's leg and on to the whale's flipper.

To test this, Dr. Karen Sears measured the adult and fetal shoulderblades of a dozens of marsupial and placental mammals, and performed a statistical analysis of the changes in shape.

Ontogenetic Trajectories: Growth of the shoulderblade in marsupials and placentals. The ontogenetic trajectories of individual marsupial and placental species are plotted in a morphospace representing general scapular shape (PC2 and PC3 are the 2nd and 3rd principal component; the first principal component is just size). Marsupials, with the exception of the bandicoot Isoodon, are represented by solid black arrows (w, Macropus [Tammar wallaby] t, Trichosurus [Australian possum] m, Monodelphis [South American opossum]). Isoodon (i) is represented by the white arrow with the black border. Placentals are represented by solid gray arrows. The ontogenetic trajectories of marsupials, with the exception of Isoodon, are remarkably similar, whereas the trajectories of placentals vary greatly.  Isoodon does not crawl to the pouch, and so its fetus does not experience the same developmental constraints as other marsupials. (Figure 7 from Karen E. Sears. 2004. "Constraints on the Morphological Evolution of Marsupial Shoulder Girdles," Evolution 58(10):2353–2370.)Ontogenetic Trajectories: Growth of the shoulderblade in marsupials and placentals. The ontogenetic trajectories of individual marsupial and placental species are plotted in a morphospace representing general scapular shape (PC2 and PC3 are the 2nd and 3rd principal component; the first principal component is just size). Marsupials, with the exception of the bandicoot Isoodon, are represented by solid black arrows (w, Macropus [Tammar wallaby] t, Trichosurus [Australian possum] m, Monodelphis [South American opossum]). Isoodon (i) is represented by the white arrow with the black border. Placentals are represented by solid gray arrows. The ontogenetic trajectories of marsupials, with the exception of Isoodon, are remarkably similar, whereas the trajectories of placentals vary greatly. Isoodon does not crawl to the pouch, and so its fetus does not experience the same developmental constraints as other marsupials. (Figure 7 from Karen E. Sears. 2004. "Constraints on the Morphological Evolution of Marsupial Shoulder Girdles," Evolution 58(10):2353–2370.)

As shown in the figure here, the placental mammals changed shoulder shape in many directions as they grew in size, while all of the marsupial limbs moved in the same direction. All but Isoodon, which doesn't use the shoulder during its move from womb to pouch, and so does not face the same developmental constraints.

This insight that developmental constraints can limit what evolutionary processes can produce is not new, and is well integrated into textbooks on biology and evolutionary biology (for a recent review, see J. L. Hendrikse, T. E. Parsons and B. Hallgrímsson. 2007. "Evolvability as the proper focus of evolutionary developmental biology," Evolution & Development, 9(4):393–401. For examples of textbook coverage, see pp. 352-365 of Ridley's Evolution, with sections titled: "Genetic constraints may cause imperfect adaptations," "Developmental constraints may cause adaptive imperfection," "Historical constraints may cause adaptive imperfection," "An organism's design may be a trade-off between different adaptive needs" and "Conclusion: constraints on adaptation.")

Other scientists confronting apparent biological constraints did not merely criticize, they proposed new evolutionary mechanisms which would not face those same limitations. The origins of mitochondria and other cellular structures is a case in point. The mitochondrion is the part of the cell in which oxygen is converted into usable energy. Without mitochondria, oxygen would poison every cell in our bodies, and without the molecular energy they produce, each of our cells would starve.

Our cells each have several mitochondria within them. Each of those mitochondria has its own circular genome with which it produces the proteins it needs to process oxygen. Each of the mitochondria possess two or more cell membranes, rather than the one found around all of our cells. It is impossible to imagine how a cell could exist with only part of a mitochondria, nor why a cell before the era of oxygen might have any of the unique parts present in the mitochondria found in nearly every eukaryotic cell. Even more mysterious was why the mitochondrial genome should be so different from that of every eukaryote. It is much more similar to that of a bacterium.

In the late 1970s, Lynn Margulis proposed that the mitochondria and several other parts of the eukaryotic cell might actually be the descendants of bacteria which were engulfed by the ancestors of all eukaryotes. This would explain the odd genome, and would explain the multiple membranes. The inner membrane is like that possessed by the free-living ancestor of mitochondria, while the outer membranes are the remnants of the vacuole within which that bacterium was captured to be digested. For whatever reason, it wasn't digested, instead helping process oxygen and cellular waste into useful molecular energy.

This theory proposed an entirely novel evolutionary mechanism, endosymbiosis. While some of the endosymbiotic relationships Margulis proposed are seen as unlikely, her explanation of the origin of mitochondria and chloroplasts have become widely accepted within the scientific community. Again, her discovery could form the basis for an inquiry-based discussion of evolutionary mechanisms, and could be enhanced by evidence of transitional stages in the evolution of endosymbiosis found today. Scientists in Japan recently described one such case (Noriko Okamoto and Isao Inouye. 2005. "A Secondary Symbiosis in Progress?" Science, 310(5746):287), and researchers recently showed that a bacterium which commonly invades insect cells, sometimes integrates its genes into the host cell, exactly like mitochondria sometimes do (Julie C. Dunning Hotopp, et al. 2007. "Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes," Science [DOI: 10.1126/science.1142490]).

Explore Evolution never mentions this process, despite its obvious pedagogical value, and its utility in addressing the limits of more commonly observed evolutionary mechanisms.