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End of Chapter Questions

  1. Energy is necessary to produce the complex biochemicals necessary for information storage and self-replication, fundamental characteristics of life. Concentration increases the likelihood that the constituents of those complex biochemicals will be able to come together in synthesis reactions. Protection is necessary to maintain a chemical and physical environment appropriate for the chemical reactions at the foundation of life processes, especially when that environment is markedly different from conditions in the surrounding environment. Catalysis provides for precise control of chemical reactions, especially their sequence; without this precise control, the biochemical pathways necessary to minimally constitute life would be extremely difficult to maintain.
  2. In modern cells, the most conserved component of cellular metabolism is the ribosome, which is built on an RNA framework, requires RNA adaptor molecules to work, and in which the actual catalytic step is performed by RNA, not by proteins. In addition, RNA subunits called ribonucleoside triphosphates are involved in many crucial aspects of cellular metabolism, including being the basic energy currency of all cells and the components of electron-transfer co-factors such as NAD and FAD. (Other recent research has found that cells contain several previously unknown types of RNA that play a crucial role in genotype remodeling and expression. Modern cells are now sometimes described as containing their own tiny "RNA World".)
  3. Spiegelman's experiment was one of the first to demonstrate that RNA populations could evolve. In his experiment, an RNA population was replicated repeatedly by an RNA replicase enzyme. The RNA population evolved over time, changing from a longer, more complicated structure that could infect bacteria to a shorter sequence that could not infect bacteria but could be replicated more rapidly. Beaudry & Joyce's 1992 study showed that a ribozyme from Tetrahymena could rapidly evolve the ability to cleave DNA, even though originally it had only been able to cleave RNA. Bartel & Szostak's ingenious experiment showed that RNA populations could evolve the ability to catalyze RNA synthesis, and Wendy Johnston's group has extended this line of research to evolve RNAs that can lengthen a growing RNA strand.
    "Life" has no agreed-upon definition-precisely because the boundary between nonlife and life is fuzzy. Thus, opinions differ about whether these evolving RNA populations can be considered "alive". Many would say that since these populations could not replicate themselves, they are not (yet?) alive. What do you think?
  4. To be useful in building a phylogeny of all living things, researchers needed a gene that (1) is present in all living organisms, and (2) has always been under very strong stabilizing selection, such that very few differences accumulate per year. Otherwise, the gene would have accumulated so many differences in the ~2 billion years that life has been evolving that its sequence would be unrecognizably different in distantly related groups. In addition, (3) the gene needed to perform the same function in all living things, since any changes in function could cause an acceleration in genetic divergence due to natural selection for the new function. Small-subunit rRNA gene fulfills all these criteria.
    This gene, however, is useless for comparing groups of mammals to each other. Why? Because it changes so slowly that all mammals still share virtually exactly the same sequence. The very feature that makes it so useful for studying ancient phylogenies invalidates it for studying more modern phylogenies.
  5. The small-subunit rRNA analysis revealed that life on earth is best separated into 3 groups, not five; and that the "protists" and "bacteria" (which originally included the "archaeabacteria") need to be revised. Protists turn out to be several different groups of tiny eukaryotes that are not closely related to each other at all. The "archaeabacteria" turn out to be a distinct group, and one that is probably more closely related to eukaryotes than to other bacteria. Plants and animals, on the other hand, are valid monophyletic groups. The fungi require a relatively minor revision-removal of the slime molds, which turn out to be an unusual group of eukaryotes. (This comes as no surprise to fungi researchers, who have always been rather puzzled by the peculiar biology of the slime molds.)
    The small-subunit rRNA tree is now recognized to be only one of many possible trees, due to extensive lateral gene transfer among early organisms. However, whole-genome analyses indicate that the basic outlines of the tree are probably valid.
  6. The "universal gene-exchange pool" hypothesis proposes a time when genomes were modular, and when organisms assembled their genomes from a common pool. It is not yet clear whether this system is stable and feasible, or whether it could give rise to Darwinian natural selection.
    The ring-of-life hypothesis proposes that eukaryotes arose from a fusion of archaeans and bacteria. However, this hypothesis cannot explain where eukaryotes got their unique genes, and how fusion could have occurred in the two groups that lack a cytoskeleton.
    The chronocyte hypothesis proposes that eukaryotes arose from a long-vanished lineage of "chronocytes", one of which engulfed an archaean that became the eukaryotic nucleus. No such chronocytes exist today, but perhaps the eukaryotes' unique genes represent a remnant of the genome of a chronocyte ancestor.
    Finally, the "three viruses, three domains" hypothesis integrates viruses into the picture, proposing that (a) viruses are a remnant of the RNA World, (b) viruses evolved DNA during arms-race coevolution with their hosts, and (c) three such viruses then converted the three domains from RNA to DNA. Evidence from viral genomes offers a modest amount of support for this hypothesis, though more viral genomes are needed to thoroughly test the hypothesis.
    These four hypotheses offer creative and varied ideas for the solution of the puzzle of life's origins. Which of these four is true, if any, we cannot say yet. But the more we learn, the more it appears that the early history of life on Earth was strange indeed.
  7. The discovery of organisms that obtain their energy from the inner heat of the Earth definitely expands our concept of the range of conditions under which life might evolve and persist. In particular, attention has focused on some of the large moons of the largest planets (Saturn and Jupiter). Some of these moons are known to be tectonically active, perhaps due to gravitational effects from their enormous host planets. If they are tectonically active, and/or if they contain sufficient radioactive elements, they should have subsurface, internal heat that might, conceivably, support life. Such life could be completely independent of solar energy.
  8. Life appeared within about a billion years of the origin of Earth. It appears, in fact, life appeared almost as soon as it was able to-as soon as cosmic bombardment ended. However, evolution proceeded relatively slowly after that. Eukaryotes appeared about 2 billion years after the origin of Earth, but remained quite small and simple for a couple billion more years, until the time of the Cambrian explosion. Intelligent life such as humans (as well as other large-brained species such as apes, dolphins, parrots, etc.) arose only within the last million years. If we start "counting" with the earliest possible origin of life at about 3.8 billion years ago, then intelligent life took nearly 3.8 billion years to evolve. Furthermore, for 99% of humanity's existence on earth, we have been non-technological hunter-gatherers. The use of radio, for example, has occurred for only the last 100 years (or so) of humanity's ~500,000-year existence. Our planet, though it has housed life for 3.8 billion years, has only been sending out radio signals for about 100 years.

    To the extent that the origin of life is a simple probability game, then the fact that it arose on Earth as soon as conditions were at all favorable, coupled with the enormous number of solar systems in the universe where such conditions might exist, suggests that the probability of it arising elsewhere is high. However, if the Earth's history is at all typical (which we have no way of knowing), we can speculate that extraterrestrial microbes are probably abundant, but extraterrestrial advanced civilizations that use radio are probably exceedingly rare.
  9. The lack of a truly universal genetic code doesn't refute any of the panspermia hypotheses. Variation in the genetic code could have evolved after introduction of the "original" genetic code to Earth; or different genetic codes might have been introduced by different panspermia events. Unfortunately, because we can't evaluate panspermia's assumptions directly (we don't have the technology, for example, to explore the planets and moons in our own solar system for life that could serve as the progenitor of life forms on Earth), all panspermia hypotheses are extremely difficult to refute. And, because it relies on extraterrestrial intelligence, it's hard to envision any observation we could realistically make that would refute directed panspermia. Panspermia, whether or not it is plausible, is currently not a testable hypothesis.
  10. These were presumably nucleotides in which the mutations that had been introduced were detrimental, not beneficial. The mutant forms were apparently eliminated by purifying selection, and only those ribozymes with the original wild-type nucleotides at those positions were able to function. (Some other nucleotide sites show mild accumulation of mutations that are probably due to genetic drift.)
  11. The tag sequence allowed selection to occur. The tag caused any pool RNA with the desired catalytic activity to be preferentially bound to an affinity column, allowing the scientists to separate these molecules from those that lacked the catalytic activity. The affinity column was, in effect, the selective agent determining which nucleotides would form the next generation in the selection experiment.
  12. The intermediate stages between the formation of simple organic compounds and complex biological polymers seem to be poorly characterized; the problems of chirality and activation and catalysis seem to be particularly difficult to solve. One general problem seems to be that the chemistry of organisms is actually fairly precise and narrow (we use a vanishingly small percentage of the possible kinds of each of our major building blocks, for example) compared to the much more complex and variable world of organic molecules that exists outside of living systems. (Readers might consider some other step to be the least characterized step.)
  13. If an organism had primitive ribosomes that contained rRNA, it should be possible to at least place it on Figure 17.18 phylogeny, since the organism might have a small-subunit rRNA gene. The placement might be incorrect, however, if the function of this primitive ribosome is markedly different from typical ribosomes. That's because differences in function can cause rapid divergence of genetic sequences due to natural selection, not to neutral evolution, whereas phylogeny analyses assume that all sequence differences occur at the clocklike rate of neutral evolution.
    If the organism had no ribosomes, it clearly could not be placed on a tree based on ribosomal RNA. If it had no ribosomes, it would be unlikely to use tRNA, so it couldn't be placed on a tree based on tRNA synthase genes, either. This is the case with viruses, which are indeed difficult to place on many phylogenies because they lack the appropriate genes.
    It is conceivable-perhaps likely, given how little we know about most viruses-that undiscovered primitive life forms exist, and that some of them might not have the necessary genes for placement on some of these deep phylogenies. If that were the case, we would have to reconsider the reconstruction of the cenancestor to take that organism's characteristics into account. We would have to be sure, however, that its differences truly represented ancestral characters, not derived ones, which would be extremely difficult without an outgroup for comparison.
  14. The discovery of organisms with a single DNA polymerase suggests that the condition of having multiple DNA polymerases may have evolved by gene duplication, with specialized DNA polymerases conferring greater efficiency of replication. We would need to know more about the distribution of single vs. multiple polymerases, especially among the three major domains, to begin to test this scenario. If, for example, archaeans such as Methanococcus have a single polymerase while both true bacteria and eucarya have multiple polymerases, two explanations are possible. Either the bacteria and eukarya evolved multiple polymerases independently, or the condition in Methanococcus represents a reversal. If, on the other hand, only the eucarya have multiple polymerases, the condition may have arisen only once. Finally, if the condition is distributed among the three domains, it could have arisen via horizontal gene transfer.
  15. The best thing to do in this case would be to enlist the aid of qualified geologists and biogeochemists! (Collaboration is one the key tools of modern science.) The rocks would first need to be accurately dated; the chances that they were much older than 3.7 billion years are relatively slight and accurate dates would be crucial. We could look for chemical signatures of life such as elevated C12:C14 ratios. Such signatures would, however, constitute relatively weak evidence that life was present so long ago. Presence of incontrovertible microfossils would be stronger evidence-but are highly unlikely, given that most rocks that old have been exposed to conditions of extreme heat and pressure.
  16. The answer to this question is left to the reader.
  17. a. The tree-of-life phylogenies show clearly that, at one time, it was extremely common for genes to cross the species barrier. The "species barrier", in fact, may not have existed, and gene transfer was apparently more the rule than the exception. Lateral gene transfer continues to be quite common today among bacteria and archaea, and occurs occasionally in eukaryotes due to viruses. Therefore the "unnaturalness" of gene transfer, by itself, is an illogical argument against genetic engineering. (This does not negate other potential arguments.)
    b. Genetically engineered modern organisms are far more likely to survive in the wild than are self-replicating RNA life forms. This is because genetically engineering modern organisms retain, from their original genomes, a sophisticated battery of other genes that may allow them to survive and thrive in a variety of modern environments. In contrast, any young population of self-replicating RNA molecules would almost certainly be eaten instantly by bacteria the moment it "set foot" in the outside world, because it would lack all of the defenses that other existing life forms have evolved over the eons. If protected from being eaten, it would likely starve, since it would be dependent on a pool of abundant, easily accessible inorganic compounds for its metabolism-and these no longer exist in most modern environments.
    c. The answer to this question is left to the reader.

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