Class #4: Cladogram!

So far, we have considered how broad the definition of life is, inhabiting moons and planets in our solar system, at least 10,000,000 exoplanets in our Milky Way galaxy, one of 176 billion galaxies in a universe 13.8 billion years old. We can analyze starlight, measuring its spectrums to identify chemical precursors for life, chemicals that react with each other to yield energy for living organisms, without light or oxygen. Life can thrive on Earth three miles deep in our oceans near hydrothermal vents spewing arsenic and sulfuric acid at 250° F. We can draw lines in the sands of 4 ½ billion years, marking geological periods of the Earth’s time in this universe. Scientists know these facts from using space telescopes, geologic strata, carbon-14 dating, and DNA clocks.

We then quickly turned to genetic technologies, due to the plethora of news stories last week about DNA barcoding and 3-Person babies.  The chromozomic conundrum of designing babies, identifying genetic disorders on the human karyotype gene map, down to the cytogenic and molecular locations.

In tonight’s class, we will learn a poquito of scientific language, namely naming elements and chemical compounds.  We will then learn how to translate DNA nucleotides into protein amino acid chains.

HaeckelThe big topic tonight will about the “Tree of Life.” Cladograms of species, like karyotypes, allow us to spatially arrange pieces of information to tell a large story.  Life change over the geological history of Earth — early on, the first living things developed into three categories, or domains, known as Bacteria, Archaea and Eukarya. In later geological periods, each of the Domains developed subdivisions, or Kingoms, one of which circumscribes all animals (Animalia).  Here’s how the entire classification process works.  And here are 3 examples.  Finally, here are two websites that describe DKPCOFGS in depth:

Next week, you will be sharing out the results of your homework assignments to the class.  The rubric follows.



Some Midterm questions will be based on these student presentations.  So take good notes.  Finally, tonight’s homework.

Homework #4

  1. Identify the DKPCOFGS of the species you chose for Homework #2.
  2. Complete the DNA translation worksheet.
  3. Translate the inorganic chemical formulas into words.

Extra credit:

  1. Once the professor says your Genetic Disease form is completed correctly, do another.
  2. Find a news article about thermophiles or extremephiles.

Class #3: DNA Technos Rule the News

I’ve decided to jumble the content today due to two news flashes this week:

  1. DNA barcoding.  This genetic technology is so simple, even even high school kids can use it to identify “sheep’s milk cheese” made from cow milk, “venison” dog treats made from beef, and “sturgeon caviar” that was actually Mississippi paddlefish.  It can be used to identify illegal wildlife trafficking and track food brands.  But yesterday, the technology was used by the New York State Attorney General’s office to conclude that:

    … top-selling store brands of herbal supplements at four national retailers — GNC, Target, Walgreens and Walmart — and found that four out of five of the products did not contain any of the herbs on their labels. The tests showed that pills labeled medicinal herbs often contained little more than cheap fillers like powdered rice, asparagus and houseplants, and in some cases substances that could be dangerous to those with allergies.

    Gingko, St. John’s Wort, and Echinacea were some of the species test for in the branded herbal supplements.

  2. 3-Person Babies” are now legal in the U.K.  Ethical issues such as “designer babies” are associated with such genetic technologies.

Tonight we’ll learn about the basics: DNA transcription/translation, mitosis, and the relationship between DNA, genes, chromosomes and genomes/karyotypes.  More importantly, we’ll pursue the ethical issues involved with genetic technologies and genetic disorders.  We’ll use the movie, GATTACA as a reference point for the class homework.

Homework #3

Suppose you and your mate are going to have a baby.  Answer the following questions, reflecting upon what we discussed in class.

  1. For your in vitro baby, would you
    1. Want to know if your fetus had genetic disease
      1. Severe, Life threatening
      2. Appearance based – skin/eye color, baldness
      3. Behavior based – alcoholism, psychotic, depression


    2. Terminate/remediate – gene therapy
  2. For you, would you
    1. Want to know which genetic diseases you are predisposed to
    2. Want gene therapy

Additionally, complete one genetic disorder worksheet, using the Genetics Home Reference website, the OMIM reference number and GeneCards to complete the worksheet.

Finally, find a news article about genetic technology (preferably one of the ones discussed in class) that you find interesting, summarize it, and include its URL (http://…) in a comment to this post.

Class #2: Earth Eras Evolve

So far, we have looked at possible life-supporting exoplanets.  As of yesterday, the oldest Earth-sized planet, currently named Kepler-444, we know of in the Milky Way is over 11 billion years old.  For the rest of this course, we will focus our attention towards life on our planet, Earth.  Our Earth is a youthful 4 1/2 billion years old.  We know its age because the oldest rock on its surface has been found in Jack Hills, Australia. Zircon 74 is 4.37 billion years old.  Formed a mere 160 million years after the formation of the solar system, its ancient existence proves that almost as soon as the Earth formed, there were seas if not oceans of liquid water on its surface, one of the essential building blocks of life.

Geologists have delineated different Eons, Eras, Periods, and Epochs of the Earth’s life to help identify key stages in the evolution of life on this planet.


The zircon crystals mentioned above were formed in the Archean Eon (3.8 — 2.5 billion years ago).  Before the end of the Archean Eon, life had been established through the planet.  Stromatolyte fossils have been dated back to 3.5 billion years ago.

The Miller-Urey experiment is a way of showing how early life on Archean Earth may have been formed. This experiment is one of the fundamental chemical reactions included in the study of exobiology.  That is, all of the the chemical reactants used to produce amino acid products are known to exist in outer space.  An alternative hypothesis for the origin of life is that these chemical reactions occurred miles below the Earth’s surface, where thermophiles and extremxozymes lurk.

The beginning of the next Eon, the Proterozoic, offered evidence of new biochemical reactions, primarily resulting in vast ranges of banded iron, the diagenesis of iron minerals throughout the Earth.  “Snowball Earth” then ensued.  And yet, 100 million years later, 635 million years ago, life not only survived, but diversified into multicellular organisms, in the Ediacaran Period.

Each of the millions of Earths in our Milky Way galaxy has its own epochal story to tell, if we ever set foot on them.  For now, we are limited to exploring the stories our own Earth has to tell.

Homework #2:

We ended class in the Ediacaran Period.

  1. Working in pairs, choose another, more recent period to research.
  2. Type in your choice as a comment to this post (first comment gets it)
  3. Begin researching the forms of life that existed on Earth during that period of time.  Post any interesting websites as additional comments.
  4. Organize your research by the 7 Properties of Life defined on page 2 of your textbook (Miller, 7th Ed.)

Class #1: ¿Que Es La Vida?

georgeGeorge Harrison tells us that life without love is meaningless.  We can debate the relationship between those two four-lettered L-words, but there can be no doubt that our emotions cloud our perspective as to what life is, and is not.

Life must be contained within the boundaries of the universe. The mechanical eye of Planck space telescope has focused on the afterglow of the Big Bang, allowing scientists to calculate its age to be 13.82 billion years old. During its life a billion trillion stars forming the hundreds of billions of galaxies , many viewed by the Hubble, Herschel and Spitzer space telescopes, flying through the night skies.  Tens of millions of life sustaining worlds may exist in our Milky Way galaxy alone. Given there are in our universe.  1,804 confirmed planets, eight of them discovered a couple of weeks ago, believed to be in the “Goldilocks” zone.  Many more are archived.

What about life in our own solar system? Water even exists on Mercury, where the average temperature is over 332 degrees Fahrenheit. Methane is periodically released from Mars, and its rock strata suggests a time where water flowed freely on its surface.  Of our 336 moons, IoEuropa, and Enceladus are likely to harbor life.

Where else can we find life?  Another moon or exoplanet?  Tell me something I don’t know, and post comment below with a link and your name.

Gliding out on the rings of Saturn

Encedalus, Titan and the rings of Saturn


I learned something new this year, we all did. It started with a picture from NASA in 2012, but its full meaning wasn’t revealed until this year, in magazines like Scientific American and Nature.  When I showed the picture above to my students, I realized after half a minute that they didn’t understand what they were seeing: Saturn’s rings on their side, its moon, Enceladus in the foreground, Titan in the background, and a tiny moon to the right of its rings.  In the future, our kids will see it, know it, as if we always knew what it is, when the truth is we only saw for the first time this year, and a lot of us couldn’t make sense of it.

galileo's drawing of Saturn's ringsThe first person to see Saturn’s rings was Galileo Galilei.  When he drew what he saw, even he couldn’t figure out he was looking at rings. More importantly, simply drawing a heavenly object going around another heavenly object was heretical. The notion that something (the rings) went around something other than the Earth (Saturn) violated a millennium of church doctrine and during the Inquisition, that was a very bad thing.  Galileo was led to the church dungeons, and was forced to view torture instruments, the unspoken word being that he would feel them as well if he did not recant. He did, and then, as the story goes, mumbled eppur si muove — “and yet it moves.”

Eventually the church police power waned, although it’s flexing its muscles against scientific facts more and more these days.  Once it was OK to see Saturn’s rings, for four hundred years we wondered how they got there.  And then this year the Cassini spacecraft scanned Enceladus, and radioed back the data which gave us the answer: the moon has an underground lake that may even nurture life.


Can you imagine standing on one of Saturn’s tiny moons, watching Saturn’s massive weight pull and squeeze Enceladus like a mother’s hands on her pimply child’s face until some subterranean mist squirts out from an underground lake, wafting into Saturn’s rings? And that the accretion of geysered mists from Enceladus over four billion years formed Saturn’s rings? Every day, year, century, millennia, we see, first not understanding or accepting something new about the rings, rings a couple of billion years in the making.  The rings will always defy human understanding, a promise that what we think we know now will change, that the mysteries of the universe will continue to surprise us, shock us into new ways of viewing our world and others.

I was in downtown Brooklyn today, at WordCamp NYC 2014, maybe that’s why I heard Walt Whitman’s words wafting down the streets:

WHEN I heard the learn’d astronomer;
Encedalus methane plumeWhen the proofs, the figures, were ranged in columns before me;
When I was shown the charts and the diagrams, to add, divide, and measure them;
When I, sitting, heard the astronomer, where he lectured with much applause in the lecture-room,
How soon, unaccountable, I became tired and sick;
Till rising and gliding out, I wander’d off by myself,
In the mystical moist night-air, and from time to time,
Look’d up in perfect silence at the stars.

Thanks Walt, you made my day.