Sorting Out the Different Forms of Life

     During the last third of the 20th century, biologists sorted life into five kingdoms. These were Animalia, Plantae, Fungi, Protista, and Monera. We’re all familiar with animals, plants, and fungi, but what are protista and monera? Protista are all the one-celled creatures whose cells contain a nucleus, and Monera are all the one-celled creatures whose cells do not contain a nucleus.
      One problem with this system of categorizing living things is that it is a human system, based more on what humans see than on what is actually true about the living organisms. For instance, four of the kingdoms, animals, plants, fungi, and protists, consist of creatures made of eukaryotic cells, that is, cells with a nucleus. Yet these are grouped as if they were as different from one another as all of them are from the monerans.
      For a long time, the members of monera were thought to be “bacteria and blue-green algae.” Eventually, researchers realized that those “blue-green algae” were actually photosynthetic bacteria. So actually, Kingdom Monera should simply have been called “Kingdom Bacteria.” But then, in the late 1970’s, a biologist named Carl Woese announced a startling discovery. He had compared RNA from a number of different living types and had found that Monera actually contained two quite different forms of life.
      Woese called the two forms of monerans “eubacteria” and “archaebacteria.” Furthermore, Woese could show that the eukaryiotic forms of life were more closely related to the archebacteria than to the eubacteria. Woese proposed that above the “Kingdom” category in the hierarchy of life forms, there should be a “Domain” category. The Domains would be Eubacteria, Archebacteria, and Eukarya, with Archebacteria and Eukarya closer together than to Eubacteria.
     For quite a long time, the rest of the biological community disbelieved and actively ostracized Woese. But now his domains are accepted and taught as a regular part of biology courses. The names of the Domains have been shortened to Bacteria, Archaea, and Eukarya. Further research has turned up intriguing similarities between eukarya and bacteria, and between eukarya and archaea. Obviously, clues about the evolution of eukaryotic cells provide plenty of work for evolutionary biologists!

Woese, Carl R. and Fox, George E. PNAS, 11/1/77, vol. 74, #11, pp. 5088-90.

Searching for Clues about Cell Origins

     I planned to write three or four articles about the origin of our kind of cells. The cells we are made of are called “eukaryotic” cells, meaning cells with a nucleus inside. But this topic turns out to have a life of its own. The more I think about it or research it, the more there is to say.
      Our species, Homo sapiens, has been on this planet for perhaps 100,000 years, at most 200,000. We know this because we have been able to retrieve and date human fossils: mummies, bones, or tools.
      We can also find and date fossils of other organisms, but this gets harder to do the longer ago the organism lived. All sorts of interference occurs. An organism may die in a location where its body immediately decays without a trace. It may die and be buried in a way that preserves some parts, hard ones like shell or bone or wood. But later geological activity, like mountain building, earthquakes, volcanoes, or erosion, may expose the fossil parts to decay or may destroy them.
      Finding and dating fossils gets much harder with organisms that didn’t have any hard parts. Yet, remarkably, some of these still leave traces, including bacteria, soft. one-celled, microscopic creatures. Some cyanobacteria (photosynthetic green bacteria from as early as 3.5 billion years ago) left stromatolites for us to find. These are stacks of calcium carbonate deposits that resulted from photosynthesis reactions. Photosynthesis removed carbon dioxide from the sea water in which the photosynthetic bacteria lived, and tiny particles of calcium carbonate powder resulted. This calcium carbonate deposited on top of the bacteria. As the bacterial cells reproduced by splitting in two, new cells remained on top of old cells. Cells by the thousands and millions and billions stacked up, and calcium carbonate deposited on each layer. And that’s what stromatolites look like. They look like rock built up out of layers and layers of material.
      Other such soft, one-celled, microscopic creatures left fossil traces. But a huge number did not. And even the traces we find may not tell us much about the inner workings of these single cells. So the puzzle is: what was going on inside the earliest cells to ever live on earth? We want to know, because we want to follow their evolution. There are clues. But these clues are a completely different kind of “fossil.” I’ll begin to talk about them in my next article.

Yet More about Cell Evolution

     In my last article I wrote about the endosymbiont theory, and I mentioned that certain organelles in eukaryotic (nucleated) cells, the chloroplasts and mitochondria, seem to be descendants of ancient bacteria. The chloroplasts are very similar to certain photosynthetic bacteria, and they perform photosynthesis in plant cells. The mitochondria are very similar to certain bacteria highly efficient at harvesting energy from various energy-rich molecules, and mitochondria perform the same function in plant and animal cells.

     Lots of mysteries remain. Did other organelles descend from ancient bacteria? If so, what is the connection? If not, how did such organelles evolve. Eukaryotic cells contain movable skeletal structures, flagella for swimming, packing and shipping structures, digestive organelles—plenty of evolutionary mysteries. But a major question is Where did the nucleus come from and how did it come to its present structure? According the the endosymbiont theory, somehow the nucleus, chloroplasts, and mitochondria came together into a permanent symbiotic relationship. We know of likely bacterial ancestors for the chloroplasts and mitochondria, but what about the nucleus?

      A nucleus in a present-day eukaryotic cell contains lots of, non-circular chromosomes—the number depends on the species. For instance, each fruit fly nucleus contains four pairs of chromosomes, each human nucleus contains twenty-three pairs. The chromosomes consist of DNA wrapped around histone proteins like thread wrapped around a spool. When genes on this DNA need to be copied into RNA, the DNA containing those genes unwinds.

      The nucleus itself is enclosed in a double membrane that keeps the nuclear contents separate from the cytoplasm of the rest of the cell. This double membrane is peppered with pores to allow certain molecules through. RNA copies of genes, for instance, pass through such pores, out of the nucleus and into the cytoplasm. There they conduct the business of producing cell proteins.

      The nucleus also contains apparatus and molecules for duplicating and dividing the chromosomes during cell-division, molecules for editing and perfecting copies of DNA and RNA, and much, much more. This complex organelle, the nucleus, like the chloroplasts and mitochondria, must have descended from some kind of prokaryotic cell. But is this ancestor still around? If so, we haven’t found it, though some biologists are searching hard.

Cells: An Evolutionary Tale

         Since the 1960’s, we have discovered a lot about the evolution of cells.

         Fossil evidence indicated that bacteria had not only been the first living creatures, but they had had the earth to themselves for two billion years. Bacteria are single-celled organisms. Each one carries its genes, made of DNA, in a ring-shaped chromosome folded up in a special region of the cell. Smaller rings of genes, called plasmids, sometimes accompany this chromosome.

         Over two billion years, plenty of mutations took place in bacterial genes, resulting in vast numbers of different bacterial species. Also, being single-celled, bacteria were, and are, capable of picking up chromosome fragments from one another, introducing even more new species.

         About a billion and a half years ago, a new type of organism appeared in the fossil record. Like bacteria, they consisted of single cells. But unlike bacteria, these cells carried their chromosomes enclosed within a special membrane. These membrane-enclosed chromosomes formed a “nucleus” in the new cell type. To distinguish bacteria from the new cells, biologists call bacteria “prokaryotic,” meaning “before the nucleus;” and they called nucleated cells “eukaryotic,” meaning “true nucleus.” Besides the nucleus, the new eukaryotic cells contained a number of infinitesimal organs, called “organelles.” Some of these organelles were photosynthetic and made sugar from light energy. Some did the opposite, extracting energy from sugar to run cell processes.

         Over the next billion and a half years, mutations and gene trading resulted in vast numbers of new eukaryotic species. In some cases, eukaryotic cells joined into multicellular species, such as plants, animals and fungi.

         As François Jacob famously wrote, evolution acts like a tinkerer. Old devices and mechanisms get put to new uses. So it was unlikely that eukaryotic cells had sprung up on their own. It was much more likely that they had somehow evolved out of prokaryotic cells.

         In 1967, Lynn Margulis at Boston University suggested that the first eukaryotic cell could actually have been a group of prokaryotic cells that began living together. In fact, she found that the photosynthetic organelles, called “chloroplasts,” are quite similar to certain photosynthetic bacteria. She also found that the energy-harvesting organelles, called “mitochondria,” are quite similar to certain oxygen-using bacteria. And it turned out that chloroplasts and mitochondria have their own genes, exactly as we might expect, if they were actually bacteria that just happened to be living inside another cell. Margulis’ idea is called the “endosymbiont hypothesis” or the “endosymbiont theory.” It is the beginning of some interesting stories about cell evolution. Stay tuned!

A Little Truth about Genes

I am amazed at the inventiveness of early researchers in pursuit of the secrets of heredity.  With no idea of the true chemistry of genes, investigators designed experiments to reveal genetic facts.

          Geneticists of the 1930’s and ‘40’s believed, incorrectly, that genes must be made of protein.  Yet during this time, George Beadle made his “one gene—one enzyme” discovery.  The discovery came about because Beadle wondered what genes actually do in order to cause traits. 

          First Beadle investigated fruit fly eye colors.  Normal eye color in these flies is a deep-red mixture of red and brown pigments.  Two bright-red mutant colors are vermilion and cinnabar; these contain no brown.  From mutant larvae, Beadle transplanted vermilion and cinnabar eye discs into normal larvae.  The eyes developed normal color in the adult flies.  Cross-mutant transplantation showed Beadle that the brown pigment resulted from a series of chemical reactions: a starting substance got changed to vermilion, which got changed to cinnabar, which got changed to brown.  Each mutant lacked one of these reactions, but it was time-consuming to figure out which one. 

          To speed up his investigation, Beadle switched from fruit flies and eye colors, to red bread mold  Beadle X-rayed the bread mold to cause mutations, then tested spores from the mold to see if they could grow on a minimal food containing only sugars and salts, and the nutrients it manufactured.

          If a mold couldn’t develop on the minimal food, this meant it was missing a nutrient because of a mutation.  Beadle tested to see if the mutation was in a single gene.  If so, Beadle then added a supplement, such as a vitamin or an amino acid.  If that didn’t make the mold grow, he tried a different supplement, until he found the missing nutrient.

          During growth, each mutant mold accumulated a chemical.  This chemical came from the reaction step where the mutant got stuck.  The mutants could be arranged in order, according to where they got stuck, and this order showed the reaction steps in the manufacture of the supplement nutrient.

          Beadle knew that each chemical reaction is controlled by an enzyme.  So each mutant mold must be missing the enzyme that could change its accumulated chemical to the next one in the series.  Since each mutant was missing a single gene, each of those genes must give rise to a single enzyme.  “One gene—one enzyme!”