Class #4: Phylogenetic it or Forget it

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 the light of the 10,000 billion billion stars around our Earth, measuring their spectri to identify the chemical precursors for life, chemicals that react with each other to yield energy for sustaining life, even 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 of time, 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.

How can scientists possibly make sense out of 4 billion years of life on Earth?  Life formed from carbon and oxygen fused from hydrogen in stars that lived and died billions of years before the Earth even existed?  Why was our world dominated by stromatolites for a billion years, only to recede to the acidic aquatic corners of the Earth, followed by millions of other species, who ruled the world in their day as well, only to disappear many millions of years ago, until, finally and contingently, our time on Earth began?  A common way to make sense of such an immense structure is to apply some organizing principles Boricua students are already skilled with:

4.0 Analysis. Analysis refers to the ability to break down material into its component parts so that its organizational structure may be understood. This may include the identification of the parts, analysis of the relationships between parts, and ecogrnition of the organizational principles involved. Learning outcomes here represent a higher intellectual level than comprehension and application because they require an understanding of both the content and the structural form of the material.

HaeckelThe big topic tonight will about the “Tree of Life.” Biologists have organized all living things into several “kingdoms,” each which possess several unique characteristics:

  • Animalia — obtain energy from other organisms
  • Archaea — many live in extreme environments
  • Bacteria — lack a cell nucleus and organelles
  • Chromista — chlorophyll c, no starch. Brown pigments
  • Fungi — a system of filaments which produce spores
  • Plantae — produce their own food through photosynthesis
  • Protista — unicellular, complex internal structures and carry out complex metabolic activities.
  • Viruses — small infectious agent that can replicate only inside the living cells of an organism

From these fundamental categories, further delineations can be made by using a taxonomy hierarchy (kids prefer cheese over fried green spinach):

  • Domains
  • Kingdoms
  • Phylum
  • Classes
  • Orders
  • Families
  • Genus
  • Species

Using this structure, we can place living and extinct species into one massive organizing structure, usually through a dichotomous key.  Several websites listed below attempt to document the ongoing efforts of scientists to complete this endeavor.

Cladograms of species, like karyotypes, allow us to spatially arrange pieces of information to tell a larger 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.

Homework #4

  1. Go to the PBS NOVA Evolution Lab.  Follow the instructions to complete the six phylogenic trees. When you finish one, print out the complete screen like the one below for credit. Make sure the date is printed out on the page (if it’s not I won’t accept it), and write your name on it.
    complete
  2. Use the Encyclopedia of LifeTree of LIfeCatalogue of Life to determine the place of your group’s prehistoric organism in the Tree of Life.
  3. Complete the Genetic Disease Worksheet.
    genetic_research_1 genetic_research_2

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: The Body Genetic

Tonight we will look at how living things develop the way they do: through their genetic code.  One way to get into this very complex mechanism is to begin with the 20 amino acids.  All living things (that we know of) are composed of these simple chemical structures that only contain carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur (CHONPS).  From these 20 simple chemicals (made up of only 6 elements) spring forth every possible living expression known on Earth.  Your dog’s hair, the flowers on a tree, the scales on a fish — all of these are composed of amino acids, nothing more or less.

How these various amino acids are arranged to make an eye or arm is determined by the genetic code stored in each and every cell of our bodies.  In the nucleus of our cells is stored our karyotype, 23 pairs of chromosomes, each one composed of hundreds of genes, or alleles, the genes built from the genetic bases codes: adenine-thymine, guanine-cytosine.

Each of our cells receives this information when it splits itself into two daughter cells, a reproductive process called mitosis.  A special type of cell reproduction, meiosis, occurs when a female egg is fertilized with male sperm.  This is the genetic mechanism which allows for the diversity of life, called “crossing over,” which occurs at a chiasma of a chromosome..

 

 

Codon coding

Punnett Squares

Please answer these following questions on the blank worksheets provided in this week’s class.

Question #1:

In pea plants, yellow peas are dominant over green peas.

Use a Punnett square to predict the genetic outcome (offspring) of a cross between two plants for yellow peas that yield a small amount of green peas.

Question #2:

The long hair of persian cats is recessive to the short hair of siamese cats. Complete a Punnett Square when a a purebred persian is mated with a purebred siamese cat.

Question #3:

The black coat of persian cat is dominant to the brown and tan coat of siamese. Complete a Punnett Square when a a purebred black persian is mated with a purebred brown siamese cat.

Question #4:

In four o’clock flowers, red plants are purebred for the dominant allele (R) of the gene for flower color. Plants with white flowers are purebred for the recessive (r) allele of the same gene. Plants with pink flowers have one of each of the two alleles. Complete a Punnett square that is expected when plants with pink flowers are intercrossed.

Question #5:

In humans, brown eyes (B) are dominant over blue (b). A brown-eyed man marries a blue-eyed woman and they have three children, two of whom are brown-eyed and one of whom is blue-eyed. Draw the Punnett square that illustrates this marriage.

Suppose one of the brown-eyed children marries someone with blue eyes. Use the second Punnett square to predict their offspring.

Chromosome Map

 

Homework

Here are some good Punnett practice problem sites. In fact, the problems above (and likely the questions on the midterm) come from these sites.

The Association for Biology Laboratory Education has a really good .pdf handout on the step by step procedure to solving Punnett square problems.Here is my own list:

If you’re daring, try the challenging Berkeley University problems (the answers are here)

So practice, practice, practice… Bring any problems you have difficulty with to class, and we’ll work them out together.

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

Class #2: I’m not old, I’m 4 billion years young!

In our first class, we looked at possible life-supporting exoplanets and moons.  We have numbers to hold onto when answering the question: is there life out there?  These numbers included the following: the universe is 13.82 billion years old, there are 176 billion galaxies in it, 10 billion billion stars in it, at least 10 million Earths in our Milky Way alone.  These are real numbers, based on radio and space telescope data, culled over decades of scientific inquiry.

As we move through this course the question will be surely raised whether these numbers or other numbers presented in class are opinion or facts.  We scientists must be more aggressive in responding: where are your scopes, your robots in space, your experimental results?  Just last week, the “War on Science” was ratcheted up another gear in the House of Representatives to effective gut global warming research.  When you can’t contend with numbers, shut off the funding.  The numbers are real, and they’re here to stay.

For the rest of this course, we will focus our attention towards life on our planet, Earth.  Each class will likely elicit more personal feelings about our place in it.  For scientists, our frame of reference is the cosmic calendar.  Whether or not you are a scientist, you should at least respect the care and effort scientists collectively make to gather data, render observations, and draw published conclusions to be evaluated by other scientists.  To debate any part of the scientific endeavor is to question all of it.

As of last month, the oldest Earth-sized planet, currently named Kepler-444, we know of in the Milky Way is over 11 billion years old.  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.

Geological Time


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.

Color_RGBEmulator6_Oct2010

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 extremozymes 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 groups, choose another, more recent period to research.
  2. Tell me who is in your group, and which geologic time period your group will research (only one group for each period, first group 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, for scientists, must be contained within the boundaries of the measureable universe. The mechanical eye of Planck Space Telescope, focused on the afterglow of the Big Bang, radios back data to scientists, who in turn have calculated the universe to be 13.82 billion years old. Within our universe, a billion trillion stars forming hundreds of billions of galaxies fly through our night skies.  Many of these galaxies have been viewed by the Hubble, Herschel and Spitzer space telescopes.  Tens of millions of life sustaining worlds may exist in our Milky Way galaxy alone. 1,804 confirmed planets, eight of them discovered a couple of months ago, are believed to be in the “Goldilocks” zone.  Many more are archived.

There is one star we are certain is near a living planet: our Sun.  We study it a lot — we just saw a “Cinco de Mayo” flare from it two days ago. The flare was so powerful it knocked out radio stations.

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.

 

Homework #1

Consigue el libro!

The course text book, Campbell Biology: Concepts & Connections (7th Edition), is available very cheaply at the following website:

DealOz Biology I textbook

Click now!  I may make one more packet next week of excerpts of the book, but you’re on your own after that, and your grade in the class will depend on you having the book.

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

rings

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.

lake

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.

 

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