October Update

Bought a standard poodle puppy.  Bringing him home October 5, so October will be full of housebreaking, and FUN.



Entries in genetics (11)


Bobby McFerrin, Music, and the Brain, Part 2

My last post showed a video of Bobby McFerrin at the 2009 World Science Festival.  McFerrin demonstrated how his audience intuitively understood the pentatonic scale: CDEGA, a scale that leaves out dissonances.  Carl Orff, the composer of Carmina Burana, used this scale to construct musical instruments for children so they could play music together that always sounded pleasant.  Such harmonic group music encouraged them to continue playing because the experience was so enjoyable.

         The question at the World Science Festival was this:  Is music inherent in humans, and therefore genetic?  Or is music learned?  According to Bobby McFerrin, his little experiment works everywhere in the world where he has tried it.  It seems as if humans all over have an instinctive sense of the pentatonic scale.

         On the other hand, said others on the panel with McFerrin, hearing develops by week eighteen in the human embryo.  Could it be that embryos “learn” about music while still in the womb?  Do they hear the music their mothers are listening to and become acclimated to scales in this way?

         I believe it must be a little of both.  All humans, everywhere, make music.  Humans invented music.  That makes music seem inherent.  Some linguists even believe that music came before speech, and led to it.

         But if we develop in utero with some kind of genetic predisposition toward music, that would probably make us more receptive to the music we hear before and just after we are born.  With no examples, my grandchild spontaneously began dancing to music as soon as he could walk.  He turned in circles in time to the beat, and frequently asked for music to be played.

         I think music is one of the top ten wonders of the universe.  And I also think that playing music together in duets, trios, quartets, etc., in bands and orchestras, is one of the most civilized activities humans engage in.  So if we are genetically programmed for music, we are genetically programmed for civilized behavior.  How wonderful it would be if we would lean more and more away from strife and more and more toward our musical genetic gifts.


Mysteries of Cell Migration

A few months ago (July 6) I wrote about how cells gather together to create multicelled organisms or multicelled organs.  Now I’ve come across a film of a marvelous experiment showing cells gathered together and “following the leader” in cell migration.

         Here it is, a lovely example of how new techniques for genetically engineering cells can be used to learn something about how cells actually work together.

          The film shows moving border cells inside a fruit fly egg chamber.  Normally, these cells migrate together, and the researchers want to learn how this happens.  So they have engineered the cells to make a protein, called “Rac” that is light sensitive.  Whichever cell in the group has the largest quantity of Rac becomes the leader, and follows the researcher’s light.  All the other cells move right along with this lead cell.

         How amazing and wonderful.  I hope these researchers will keep learning about this.  But just the fact of the leader being the one with the most of a certain protein seems magical and mysterious enough.


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.