October Update

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




"M" Is for the Million Things She Gave Us

In a follicle in the body of a maternal fruit fly or mouse or human being lies an egg cell.

This egg cell is immense compared to the sperm that may eventually fertilize it. A sperm must race vast distances to arrive at the egg in time to compete with millions of other sperm for the fertilization prize, the chance to pass its genes to future generations. So a sperm carries only necessities: a nucleus with the genes packed into chromosomes, high energy molecules and energy-releasing structures to power the long race, a flagellum to swim with, enzymes to dissolve the egg’s protective covering and to signal that this sperm is now fertilizing the egg, and no other sperm may enter.

Once fertilized, the egg cell will divide repeatedly to produce a hollow ball of many identical cells, which will then layer themselves to start developing into an embryo. These early cell divisions happen so fast, the new cells have no time to grow before they divide again. Therefore, except for their chromosomes, which duplicate in full sets before each division, the new cells’ substance and internal structures are all portions of the original egg. So a mother animal must produce an egg large enough to provide all this material.

Next, how do the hundreds of identical new cells wind up becoming different parts of an embryo? How do they turn into head, middle, tail, top, bottom, sides, limbs? We don’t know for sure, but certain clues suggest that the maternal reproductive system conveys this body architecture. Before the egg cell leaves the follicle, molecules from the mother’s body diffuse into it. These molecules are concentrated at one side of the egg, so when the fertilized egg repeatedly divides, some of the new cells will contain a lot of the maternal molecules, and some will contain few or none. So already, the many new cells are not identical. Inside the new cells which contain them, the maternal molecules may produce proteins, and the proteins may signal the new cells to specialize in being the head-end of the embryo. Once these head-end cells specialize, they manufacture their own signals to send to other new cells farther downstream in the incipient embryo, telling them to become the embryo’s mid-section. Then the mid-section cells signal the tail-end cells. Once all these groups of cells start to specialize, they can signal within the group for finer and finer anatomical details.

So like it or not, we owe a lot to Mom.

Lots and Lots of Evolution

    In his Life of the Cosmos, Lee Smolin asks, Why is our universe hospitable to life, and why is it full of stars? Smolin proposes that the universe we inhabit is a product of natural selection: Universes have come and gone, but the most successful ones at reproducing, that is, giving rise to new universes, are the ones that are thick with stars.

    A universe full of stars will also be a universe full of carbon, the very element necessary for life as we know it. Each carbon atom forms four covalent bonds, and carbon atoms bond with other carbon atoms to form long chains, with and without branches. Lots of different atoms and ions can bond all along such carbon chains. Then the chains twist and circle into a vast variety of shapes. And molecules with charge and shape are the working machinery of living cells.

    The first stars in our universe consisted of hydrogen and helium, but as those stars burned out, they produced heavier and heavier elements. Eventually, dying stars exploded into stardust and delivered all 92 natural elements into space. Gravity pulled the stardust together, making it coalesce into new stars, sometimes with planets. One such star is our sun, and one such planet is our earth.

    At first the earth was just a huge, probably hot, ball of chemicals, mostly compounds of the 92 elements. Then the earth cooled, and another kind of evolution began. Water condensed into oceans, and some partly-soluble/partly-insoluble molecules turned their insoluble parts away from the water to form infinitesimal, floating spherical membranes.

    Trapped inside the spheres were various compounds. Many spheres burst like bubbles. But the most successful spheres didn’t burst. Instead, some of their inner compounds produced more soluble/insoluble molecules. These enlarged the membrane until a sphere split into two spheres. To do this, the material inside would need energy, perhaps from the breakdown of other enclosed compounds. Over time, some successful spheres developed ways of taking in more compounds from the ocean to break down for energy or to use in manufacturing more membrane. The longer such spheres were around, the more new, useful compounds they were able to take in or manufacture, and the more useful internal structures they were able to develop. Until eventually some of the spheres actually became very primitive cells, somewhere between life and non-life. This set the stage for yet another evolution: that of living organisms.

What Is Autism Trying to Teach Us?

The rising number of children with autism could be a warning.  Genetically, these children may be especially sensitive to some of the tens of thousands of pollutants in our environment.  

        According to Discover magazine, autism researchers have begun paying attention to the digestive and immune disturbances that accompany the personality aberrations of autism.  Autism is probably connected to genetics.  That’s “genetics,” not “a gene.”  And autism is probably connected to environment.  Like most genetic phenomena, it’s a combination of nature and nurture.

        Genes often work in teams, like this:  All your cells need a certain anti-oxidant molecule.  In each cell, gene 1 in the team manufactures the first part of the anti-oxidant molecule.  Then gene 2 in the team takes the first part of the anti-oxidant and adds a second part.  Then gene 3 adds a third part, and so on until a final gene completes the job.  When the anti-oxidant molecule—let’s call it glutathione—is finished, it can start detoxifying poisonous oxygen radicals that result from daily cell work.

        Now let’s suppose that one of the genes in the glutathione team is handicapped.  Glutathione production slows down. Or the glutathione is defective.  Either way, crowds of oxygen radicals accumulate and interfere with cell functions.  Lots of different kinds of cells suffer when this happens: digestive cells, immune cells, and brain cells, just to name a few.

        One form of suffering brought on by this excess of oxygen radicals has to do with the way cells repair damage from allergens or pollutants.    In addition to the gene team that makes glutathione, each cell has teams of repair genes.  A handicapped gene in a repair team may become even more handicapped when it is stressed by the poisonous accumulation of oxygen radicals.  So repair slows down.  When your cells have unrepaired damage, they send out calls for help, and the first thing your body does is mount a defense that includes inflammation.  If the damage remains unrepaired, the inflammation may become chronic: you get chronic digestive problems, chronic allergic problems, and chronic inflammation of the brain.

        So here and there a handicapped glutathione gene plus a handicapped repair gene might lead to what we call autism.  And the rising number of kids with autism might be an indication of what can happen to human beings in a polluted environment.


What we didn't expect from the Human Genome Project

The history of DNA research is a tale of patient researchers laboring day after day on myriad tiny problems.  It is a tale of myriad answers leading at last to profound insights.

    This is what happened with the Human Genome Project.  The question the HGP set out to answer was:

• What are all the genes in a human being?

    Before the Project began, geneticists had learned a lot.  They knew that genes work by manufacturing proteins.  They knew that genes do this indirectly:  Enzymes in the cell nucleus unroll and unzip the DNA double helix and copy a target gene into messenger RNA.  The messenger RNA carries the gene’s code to cell parts outside the nucleus to direct protein manufacture.  Finally, geneticists knew that humans have around 100,000 proteins in their bodies.  So researchers expected the HGP to take years and to turn up about 100,000 genes.

    But the geneticists working on the Project, devised new, speedier techniques for decoding DNA.  A lot sooner than anticipated, the whole human genome was known.  And there weren’t 100,000 genes—there were only about 30,000!  Or maybe only 25,000!  A humbling conundrum.

• How do the 100,000 proteins come from only 25,000 genes?

    Before the Human Genome Project, something else had come to light:  When a messenger RNA gets copied from one of our genes, it gets “edited.”  Molecules called spliceosomes cut the RNA message into fragments, remove some of the fragments, and splice the rest back together again.  The spliced message is what actually gets translated into a protein.  But the spliced message isn’t always the same.  The set of fragments that get spliced together can differ.  So that alternative proteins result from the same messenger RNA and therefore from the same gene!

    Is this how 25,000 genes make 100,000 proteins?  How did this incredible system evolve?   Some biologists think the first active catalytic molecules of life were RNA, while others think they were protein.  Intriguingly, spliceosomes have some of both.  Could alternative splicing be connected to the earliest molecules of life?  When we investigate this editing of RNA, are we seeing far back into life’s beginnings, just as we see far back into the beginnings of the universe when we investigate the oldest light we can find with the Hubble Telescope?

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