Showing posts with label science and math. Show all posts
Showing posts with label science and math. Show all posts

18 June 2011

What is the Matching Part on tRNA Called?

Originally landed on: Degeneracy of the Genetic Code

A tRNA molecule is a small strip of RNA folded into a series of loops. One end is attached to an amino acid, and the other end pairs up with the codons on an mRNA.

A codon is a set of three nucleotides, which can be any combination of adenine, uracil, guanine, or cytosine. Adenine matches up with uracil, and guanine matches up with cytosine.

The end of tRNA that pairs with the mRNA codon is called the anti-codon end, because its nucleotides are the matching opposites of the ones in the codon.


More About the Genetic Code
More About Genetic Code Degeneracy
About Micro RNA and Its Role in Gene Expression

17 June 2011

How to prepare for a science cruise on the open ocean (for students)

Students new to marine science are often not told what to expect on a research cruise. Here's some of the basics.

The Ship Has A Crew

The first thing to know is that the ship comes with a full-time crew that is paid to take care of everything not directly related to doing science. There will be a captain and mates to take the ship wherever the chief scientist wants to go, a cook to take care of all meals, etc. Pack as if you were going to stay in a hotel. You will have a bed with linens and blankets provided (on larger ships you might have your own room), and storage space for clothing and toiletries. Some of the larger ships may provide personal fridges and have laundromats.

Bring a sturdy pair of covered-toe shoes. You will be working around heavy equipment, possibly dangling overhead on a rocking ship. Bring sunscreen - there is no shade on the decks at sea. Bring a poncho in case you have to work in heavy rain. Life jackets and hardhats are usually provided.

The ship will also likely come with a marine tech. This person takes care of all the scientific equipment that comes with the ship - keeps them clean, calibrated, and in good working order. This person also works closely with the crew (winch operators, bridge officers) to put instruments into the water and bring them back out of the water.

The Obligatory Safety Drill(s)

There will be a safety briefing and a number of emergency drills shortly after the cruise starts. You will learn where things are, what to do, and where to go if you or someone falls overboard, if there's a fire, or if the ship sinks. In most cases you just have to show up in a specific part of the ship with life preserving gear, while the crew does all the important parts.

Cruise Purposes

There are a great many different kinds of science done on cruises. Some are research oriented, some are educational. Generally, all cruises are for the purpose of collecting either oceanographic data, or samples of something, which will be processed and analyzed later in a lab back on shore. Samples could be water samples for various chemical elements or nutrients, microbe or plankton samples, fish samples, sediment samples, etc. Sensor data will always include temperature and salinity. The third major purpose of a cruise is to deploy or retrieve monitoring instruments left in the ocean for months at a time. Most cruises have a combination of different purposes.

What you do on a cruise will be whatever the chief scientist tells you to do. There will probably be lots of manual labor. There may be lab work or computer work, or menial clerical work (such as making labels for samples). If it's a research cruise, expect to have a heavily altered sleep schedule, as everyone will be on duty shifts - science goes on around the clock. I've seen 12-on 12-off, 4-on 8-off, alternate every 4 or 6 hours, etc.

Recreation on a Science Vessel

You will be surrounded by nothing but water in every direction. It's lovely for the first few days and then becomes monotonous if the cruise lasts longer than that. Entertainment and recreation on board will be limited. Internet and phone are both by satellite, which is expensive, and will likely only be available for research or emergency purposes. Some ships will upload and download email once or twice per day, to be read and composed offline - assume that nothing you write or receive is at all private. If the ship goes far enough away from land, there will be no TV or radio. Cell phones will not have signal. Most ships have a small library of books and movies on video/DVD. Some of the larger ones may have exercise equipment.

About Seasickness

There are a number of ways to avoid seasickness - over-the-counter drugs like Dramamine or Bonine, Sea Band wristbands which use acupressure, prescription patches, etc. Most ships will carry an ample supply of meclizine (generic of Bonine), passed out by the ship's medic (or sometimes on smaller ships just sitting out somewhere where anyone can take as much as they want). Take a pill a few hours before the boat leaves the dock.

If you do feel sick, sit outside where you can see the horizon, on as low a level of the ship as possible. The ship sways more up top than at the water surface. If you puke, do it facing away from the wind. Remember that all the outside decks are waterproof, and the work deck has a hose somewhere for rinsing off afterward (be sure to use the saltwater hose) - you do not need to lean over the side and risk falling off the ship (not even if you think it would be a really good idea to jump overboard to stop being sick). If you do want to lean over the side, remember to wear a life jacket. Also, keep some paper towels and kleenex stashed into your pockets so you can blow your nose.

Afterward, eat starchy foods like rice, potatoes, bread. Those will help settle your stomach. Remember that seasickness isn't actually a problem with your stomach - it's your brain trying to make sense of the rocking motion. If you're unfortunate enough to be seasick no matter what you try to do to prevent it, bring along Snickers bars. Those are one of the few food items that taste just as good coming up as going down.

Deep Sea Fishing

On every science vessel I've ever been on, there is always at least one avid deep sea fisherman among the crew. Anytime no science tasks are going on, he will have a line over the side. There will probably be fresh fish for dinner at least once. If you do any fishing of your own, just remember that the science mission takes priority and to pull up your line accordingly.

Swim Calls

Depending on the organization that runs the fleet to which your ship belongs, there may be a swim call at some point during the cruise. Bring a swimsuit.

No Alcohol

All science vessels (in the U.S. at least) are dry. Do not bring alcohol.

16 June 2011

An Example of Technology Used to Study Marine Biology


a MOCNESS

a MOCNESS frame with no nets


The MOCNESS, or "multiple opening closing net (and) environmental sampling system," is a contraption with lots of individual nets, usually at least nine, which take turns opening and closing to collect plankton samples at different depths. It gets dragged behind a slow-moving boat, and it can take several hours to complete a set of collections.

It's an example of the type of technology used to study zooplankton ecology, a branch of marine biology.

More Examples Here

14 June 2011

Where does the sea horse fit on the animal kingdom chart?

Originally landed on: Life Cycle of a Seahorse

Believe it or not, a seahorse is a type of finfish. It's just heavily modified from what you might think of as a "normal" fish shape. According to the Tree of Life as of 2007, its current taxonomic (scientific) classification is:

Kingdom Animalia
Phylum Chordata
Osteichthyes
Class Actinopterygii
Order Gasterosteiformes
Syngnathoidei
Family Syngnathidae
Genus Hippocampus

There are about 40 species worldwide today.

10 June 2011

Intro Topics to Population Genetics

Population genetics is the study of genetic variation in populations, and how the variation changes from generation to generation. The most fundamental unit of genetic change is the allele. Alleles are different versions of the same gene.

One of the key questions in population genetics is: if you know how many of each allele is in a population in one generation, how will their percentages change in the next generation? An answer of "no change" is called the Hardy-Weinberg equilibrium. This theorem is an important comparison tool for finding out which genes in a genome are doing something more interesting than "neutral."

Learn more in the articles below:
What is an Allele?
The Hardy-Weinberg Equilibrium Theorem

And feel free to suggest more topics here, if you have other basic questions about population genetics. :)

08 June 2011

Is a seashell an abiotic feature?

Originally landed on: Abiotic Factors of an Open Ocean Ecosystem

The definition of "abiotic" is "non-biological." A seashell is made by a living organism, therefore it is biotic. In the sea, shells come from creatures like clams, oysters, mussels, scallops, whelks, conchs, periwinkles, and other sea snails.

While seashells are biotic, they can significantly influence the abiotic factors of their surroundings, especially the pH of water. Seashells are made of calcium carbonate, which acts as a buffer by dissolving in acidic conditions and causing pH to go up, becoming more basic.

In general, all precipitated calcium carbonate in the sea has a biotic origin. Corals use it to build massive reefs. Many types of creatures of all sizes use it to make protective shells, including microplankton. Old shells become white calcium-carbonate sand, and eventually over geologic timeframes, limestone.

In modern times, an increase in global carbon dioxide has begun to make the oceans more acidic, which makes it much harder for marine organisms to precipitate calcium carbonate for their shells.

04 June 2011

What is an Ecosystem?

An ecological community consists of all the species at a particular place in a particular timeframe, and all their interactions with each other. An ecosystem is an ecology community, plus all the physical and chemical (abiotic) factors of the surrounding environment.

Learn what each part of the ecosystem definition means in this overview.

31 May 2011

What caused the collapse of the Peruvian anchovy industry?

Originally landed on: A Brief Introduction of El Niño

Fisheries management is about calculating exactly how much fish can be harvested in a given fishery without killing all of the fish. If all fish are caught, none are left to reproduce and make more fish to catch later. Fisheries ecology is about making models that take into account everything about the life cycle of the fish, from early life history to diet to habitat use to reproductive patterns - then figuring out fishing seasons, fishing gear, size and catch limits, etc. that will allow everyone to do some fishing while harming the overall population the least.

The fisheries model for the Peruvian anchovy fishery was originally devised in the 1950s, before the nature of El Niño was well-known. It did not take into account the effects El Niño had on the fish, which was that the population was smaller. Fishermen therefore fished for them at the same harvest limits as normal years - which, during an El Niño year, is not a sustainable rate.

There was a strong El Niño in 1972. The fishery collapsed shortly after that.

Learn more about the basics of El Niño, La Niña, and the Southern Oscillation (ENSO for short), from both a historical and a modern scientific perspective in this introductory article.

28 May 2011

Insects of the World: Scientific Classification

By far the largest group of living things in Kingdom Animalia, insects are wildly successful creatures in large part because they evolved flight. There are more species of flying insects now than there are anything else that flies or has every flown, combined, including birds, bats, pterosaurs, and so on.

The briefest version of their taxonomic tree looks like:

Kingdom Animalia
Phylum Arthropoda
Class Insecta
  • Subclass Apterygota - primitive wingless insects
  • Subclass Pterygota - evolution of wings
    • Infraclass Neoptera - evolution of wings that can fold flat against their backs
      • Superorder Dictyoptera
      • Superorder Paraneoptera
      • Superorder Endopterygota - a life cycle that includes complete metamorphosis with distinct larval, pupal, and adult stages
A comprehensive overview that includes full-color photos is here.

24 May 2011

The Basics About Rocks

The Earth has three main types of rocks: igneous, sedimentary, and metamorphic. Igneous rocks form out of molten magma, then undergo weathering, which disintegrates them to form sediments and soil. Sediments can become cemented back together to form sedimentary rocks. Igneous or sedimentary rocks can also undergo additional heating or high pressure, which partially melts them and transforms them into metamorphic rocks. Finally, all rocks can melt completely back into molten magma.

Types of Igneous Rocks
How Igneous Rocks Form: Bowen's Reaction Series

Mechanical Weathering
Chemical Weathering
What Soil is Made Of and How It Forms

17 May 2011

The Little Dipper in the Night Sky

What is the Little Dipper? Where in the night sky is it located? And how do you find it while you're standing out there in the dark? If you're in the northern hemisphere, you can find out here!

(If you're in the southern hemisphere, you're out of luck, sorry.)

15 May 2011

Competition in Ecology

Competition within an ecosystem happens whenever resources are limited. Non-divisible resources lead to interference competition, which usually results in competitive exclusion. Exploitative competition tends to happen over divisible resources, leading to niche segregation - which can be symmetrical or asymmetrical. Invasion from outside the ecosystem, predation, disturbances, and changing conditions are mediating factors on competition. This article explains what all that means.

08 May 2011

How to Use a Beach Seine Net to Catch Small Fish

A seine net is a vertical net with floats at the top and weights at the bottom, which is used to surround all fish in an area. Beach seines are small, deployed by hand, and designed for use from near a shore. In contrast to cast nets, which are useful for capturing schools of small fish that you can already see from the surface and are a popular way to catch bait for fishing, a beach seine net will capture all fish within its bounds, schooling or otherwise, whether you can see them or not. This makes them more useful for science education purposes.

While you can use a beach seine net for bait fishing, you do have to get into the water. Cast nets take a bit more skill to deploy but the advantage is you stay dry on land, and each deployment is faster.

Regardless of purposes, check into fishing permits before you start to make sure whatever you're doing is legal.

Things You'll Need

  • A beach seine net
  • Two people, one of whom will be up to waist deep in the water. The wader should wear good close-toed shoes or dive boots or other similar footwear, in case of sharp items underwater.
  • Some small dip nets
  • A bucket to hold captured fish live
  • If this is for educational purposes, fish identification guides. Any fish not intended for a permanent collection can be released afterward.

    Step One

    Pick a relatively cleared part of the shoreline to deploy the net. A small beach or sandbar works best.

    While one person stands on shore at one end of the area, holding one end of the net, the other person wades straight out with the other end, as far as the net will go. Make sure that the net's weights are touching the bottom so that nothing can escape from underneath.

    Step Two

    Once the beach seine net is properly stretched out, the wader walks slowly parallel to the shore until they reach the other end of the area of interest, then walks back in to shore. The net should make a roughly U-shape in the water.

    Step Three

    Once the wader is back ashore, both people slowly drag the beach seine net out of the water a little at a time, making sure the weights drag on the bottom. All the fish will be forced up on shore where they can be captured individually with dip nets.

    Seine Nets vs. Gill Nets

    Gill nets are another type of vertical net with floats at the top and weights at the bottom. The difference between a seine net and a gill net is the size of the netting mesh and how they catch the fish. The hole size of a gill net is large enough for a fish to fit its head through, but not all the way. Gill nets rely on mid-sized, strong swimming fish to swim into the net without seeing it and get caught by their gills. The design of a seine net is to actively catch the fish, while gill nets fish passively (you set it up and wait a while, then see what got stuck in it). Another difference is where you set the net - beach seine nets are deployed from shore, while gill nets are usually set up out a ways, with a boat. (Or, if it's a larger seine net like a purse seine, you generally drive the boat around in a circle.)

    Gill nets are illegal in a lot of places for the vast majority of uses (inhumane, bird and turtle bycatch, etc). Check the local fisheries regulations before using them.
  • 16 September 2010

    Comparing the Sun and Earth

    Comparing the Sun and Earth, both are astronomical objects, but one is a star and the other is a planet. Stars like the Sun are balls of ionized gas, called plasma, engaged in thermonuclear fusion. Gas giant planets are balls of mostly gas that aren't massive enough to ignite for fusion. Terrestrial planets like the Earth are balls of mostly solid and liquid that aren't massive enough to hold enormous atmospheres of gas. In the Sun-Earth relationship within the Solar System, the Earth orbits around the Sun.

    More

    30 August 2010

    Particle Physics in Cosmology

    The Standard Model of particle physics identifies the elementary particles of matter and provides an explanation for three of the four fundamental forces of nature - electromagnetism and the strong and weak forces, using force mediating gauge bosons and a mass mediating Higgs boson particle.

    This series of articles explains it all in (relatively) easy-to-understand plain language.

    18 August 2010

    How is a Gamete Different From Other Cells in the Body?

    From a strictly genetics perspective, there are two types of cells in a multicellular body: somatic cells and germinal cells. Germinal cells make sex cells, or gametes. All other cells in the body are somatic cells. How is a gamete different than other cells in the body? Learn the two biggest differences here.

    15 August 2010

    History of Medieval Astronomy

    The prevailing cosmology throughout the Middle Ages was geocentrism, with Earth as the center of the Universe. Ptolemy published his epicycles model in Almagest in 150 CE. The medieval period of Europe is widely accepted among historians as beginning in 200 CE, after the fall of the Roman Empire, and ending in 1500. Copernicus reintroduced and expanded upon the concept of heliocentrism in Revolutionibus Orbium Celestium, published in 1543. The history of medieval astronomy, then, can be summarized as "not much happened."

    HOWEVER... the parts before and after were very exciting. :) More here

    31 July 2010

    An Astronomy Nova

    What is a nova? In terms of astronomy, it's when a star suddenly becomes a lot brighter, then dims over several months. This article explains how and why novae occur, and compares novae to x-ray bursters and supernovae.

    24 July 2010

    Is Spontaneous Self-Correction of Gene Mutations Possible?

    The short answer is yes. However, that's not as exciting as it sounds. Click here to learn more about what mutations are and how they work.