What a wonderful world

Gives me goosebumps.

Science isn't personal: Evolution

I just watched this 10 min video from Qualia Soup about what evolution is, phrased particularly as an argument against people who don't accept it. It has good narration and clear animations to explain important mechanisms of evolution and misconceptions people have about them.

It reminded me that Qualia Soup also has some other good things to say that relate to perception and science:

• open-mindedness
• skewed views of science - how personal bias can get in the way of understanding

Bird brains - song, speech, and genes

Bird brains (Nova Science)
We can learn to talk - how? Studying bird brains can help us find out. This video covers the following.

• How complex is bird song?
  Recordings slowed down sound more musical than you think, and have inspired at least one famous composer.
• What parts of the brain do birds use when singing and listening to song?
  The same parts as we use to speak and listen to speech, as revealed by functional MRI.
• Do birds stutter?
  Yes, some do! And the difference in brain function (from normal singing birds) is similar to the differences human stutterers show.
• Finding a mutant FOXP2 gene (the language gene) involved in an inherited speech disorder by studying an affected family, and then finding FOXP2 in birds and how it relates to song learning.
• The search for other genes that might explan why we can speak, and birds can sing, but other species (e.g. chimps) can't.

The science of decay

AFTERLIFE: THE STRANGE SCIENCE OF DECAY
"Decay: it happens to everything and everyone..."

In this documentary, a biologist sets up a glass box within Edinburgh Zoo and puts lots of stuff in it to see it decay: cooked rice, chilli, cups of tea, a fish, cheese, a fruit bowl, a vegetable box, a raw chicken, sausages, hamburgers, a whole pig on a spit, a compost heap, a wood pile...even a dead rat!

The process of decomposition is observed over a period of 8 weeks using time-lapse cameras and specialist photography to capture the extraordinary way in which moulds, microbes and insects are able to break down everyday things and allow new life to emerge from old.

Highlights:

• Bacteria decomposing a chicken, including how they sense and communicate with each other, and coordinate. (2 minutes)
• How the US Army stops its food going off - extreme preservation! (6 minutes)
• Why we have coal  - plants evolved wood strengthened with lignin well before fungi evolved the ability to digest it and break it down. This meant dead trees ened up lying all over the place, not decaying, and instead vulnerable to burning (especially with all the extra atmospheric oxygen from photosynthesis outpacing respiration). Masses of undecomposed / burnt wood helped to form great deposits of coal. The high oxygen levels also assisted the evolution of large insects, which otherwise have too inefficient gas exchange systems to be able to survive today, and dinosaurs! The end of the age of dinosaurs coincided with a firestorm that probably burned about 25% of the world's forests, leaving less food, less oxygen in the air, and a cooler earth thanks to ash clouds.

Too many highlights! Just watch the whole thing!

Year 11 Microorganisms links

All were active on 15/11/11

General information

• CELLS alive - A general microbes information website.
• Microbes and food - Information and illustrations about a variety of microbes and their interactions with food, in producing food, spoiling it and causing food poisoning.
• Infectious diseases – Pathogens - Good overview with structures and functions of microbes and other info. Includes Bacteria, Fungi (yeast), Viruses; (skip Protozoa and Parasites); How pathogens are spread; How pathogens cause disease; Growth of pathogen populations. Has a quiz at the end.

Decomposition and nutrient cycles

• Decay – bacteria and fungi - How decomposers decay things, and how it can be prevented to preserve foods. Info and a Test Bite
• Biological compounds activity - Interactive animation on the carbon, oxygen and nitrogen cycles (after an overview of what is in the organic molecules of proteins, carbohydrates and fats). Supported by the text revision and test here.

Fighting disease

• Infectious diseases – Immunity - Text resource supported by simple animations showing how various components of the immune system work, and also how vaccines work.Sections include: White blood cells / response to infection; Immune memory; Vaccination; (you can safely ignore Monoclonal antibodies). A quiz at the end.
• Defending against infection - Mostly text on bacteria and viruses and fighting disease. Includes a couple of great CG animations on p4 and p5 on how bacteria are fought off by the immune system cells and how vaccination works. Also a bit on antibiotics.
• Infectious diseases and their treatment - This interactive e-source about how the body copes with disease allows you to complete summary sheets to check you progress as you go. Pretty thorough and relevant!
  There are 10 sections in this e-source: Introduction; Pathogens cause disease; Immunity; A bacterial disease – Meningitis; A fungal disease – Candidiasis; A viral disease – SARS; (A protozoic disease – Malaria; you don't need to do this one); Modern medicines of the world; Appendix of diseases; Quiz
• Human immune system - This interactive e-source about the immune system allows you to complete summary sheets to check your progress as you go.
  There are 11 pages in this e-source: Introduction; Pathogens and disease; Barriers to infection; Acquired immunity; Immunisation; Medicines and the immune system; Vaccinations in the UK; Antibiotics; Immune system causes problems; HIV/AIDS; Quiz
• See HIV in action - A huge animation file about how AIDS infects the body, showing the “life” sycle of the HIV virus. Possibly slow to load.
• Making vaccines - An interactive where you follow the instructions to make 6 different types of vaccines. Wicked!
• Fighting back - An interactive animation in which you, playing the role of the immune system, try to figure out how to overcome and infection of the mumps. Also details why AIDS is so devastating.

For interest only: 

• AIDS:The Modern Pandemic - A resource-filled CBS news site detailing the worldwide prevalence of AIDS. Includes some statistics, an animation of how AIDS affects the body, the history of the disease, a photo essay on its youngest victims and much, much more! A fair bit off-topic though. 
• How Herd Immunity Works - Why it is important for everyone who can to be vaccinated. A 10 minute video.

Year 11 Mammals as consumers links

Food and what's in it: focus on carbohydrates, proteins and fats

• Biological compounds activity - Interactive animation that starts with an an overview of what is in the organic molecules of proteins, carbohydrates and fats (and then goes onto carbon, oxygen and nitrogen cycles, which is useful for the Micro-organisms topic).
• Body needs - Are you what you eat? A flash mouse-over animation to investigate your nutritional requirements. Includes details of what you get if you don’t get enough of particular nutrients. Focus on carbohydrates, proteins, lipids
• Diet and Digestion - Includes what’s in food, a nice diagram of the digestive system, an animation of peristalsis and a wee bit about physical and chemical digestion. Has an easy and a hard Test Bite at the end.

Organs in the digestive system (mostly in order of usefulness)

• Digestion - This interactive e-source about food groups and the digestive system allows you to complete summary sheets to check your progress as you go, and there’s a quiz at the end too. Really quite a good overview, so highly recommended.  
• Organs of digestion - animation with good step-by-step descriptions of wha's going on in each organ as food moves through. Was one that went with an activity in your booklet.   
• The digestive system - Short animated movie with narration.
• The real deal on the digestive system - An informative and easy to understand article that leads you through the organs involved. Updated June 2010. Has an animated diagram for a very basic review of structures and functions on page 1. 
• Food processing - Interactive showing basic processes in a highly no-scientific manner. Good reminder about what is digested where, and how, and by what, though. Pretty basic!
• Diet, drugs and health - Very basic overview, maybe even too basic? This Revision Bite covers: Nutrients; Some effects of a poor diet; Digestive system; Digestion and enzymes; Absorption and egestion (plus more).
• The Digestion and Absorption of Fats - Step-through or narrated animation. Warning: Pretty complex and thorough, but shows absorption nicely, and includes villi. Shows roles of bile and lipase acting on fat molecules too. 

Enzymes and digestion

• Enzymes and their uses - Text resource with a few diagrams and animations about enzymes. (Not very interactive!) Includes: Enzymes; Types of enzymes; Enzymes in digestion; The properties of enzymes; How do enzymes work?; Effect of temperature and pH; Uses of enzymes; Immobilised enzymes
• Enzymes - Enzymes in general and their role in digestion too. Test Bites for both.

After food has been absorbed

• Circulation - about the heart and blood vessels, briefly. Not specific to transporting nutrients. 
• Life Processes – Respiration and the role of lungs - A quick text overview of respiration and how the lungs are involved. See pages 3, 4 and 5 only. (The rest reviews muscles and bones). Bit much detail on lungs, but a couple of nice animations showing the exchange of CO₂ and O₂.
• Insulin and Glucose Regulation - How hormones from the pancreas regulate the level of sugars in the blood after and between meals. An 'Extra for experts', definitely. 

Differences between mammals

• A Cow's Digestive System - Explanation of rumination in the first chambers of a cow’s stomach, with animation and narration (as embedded above) 1:35
• Skull science - How the skull shape and teeth relate to the diet of various mammals. A brochure-type resource.

Year 11 DNA replication and cell division

THE STRUCTURE OF DNA AND DNA REPLICATION

• Genes and Inheritance  - A fairly comprehensive review of Year 11 Genetics. Mouseover specific terms to be reminded of definitions. Each page has a quiz at the end to check your understanding. Some interesting applications of inheritance with respect to genetically inherited diseases. A complete quiz at the end.
• Tour of the basics of genetics - Animations to remind you of the structure of DNA and how it works.
• Structure of DNA  - A narrated video to watch. Nice because it shows how the actual atoms in the molecule are arranged. Very complex in the vocab, so at best, just watch the pictures.
• DNA workshop: DNA replication (& protein synthesis) - Interactive animations to review the processes of DNA replication (and protein synthesis). Get involved; it doesn’t take long!
• DNA replication – This animation includes more of the nitty gritty of replication, showing the enzymes that are involved. e.g. helicase, polymerases, ligase.

HOW SCIENTISTS MADE THEIR DISCOVERIES ABOUT DNA

This isn't examined at any level, but it's still interesting!

• Meselson-Stahl experiment: DNA replication - How scientists found out that DNA replicates by unzipping and copying complementary strands.
• Decoding DNA - The science involved in decoding DNA – finding the sequence. More for 13BIO, but interesting nevertheless.
• DNA from the beginning - A huuuuuuge resource including text, animations, and a lot of the science behind the knowledge. Use the menus down the side to navigate through some of the main points of the genetics topic. Of the three main sections, Classical Genetics and Molecules of Genetics are the most relevant.

MITOSIS
Don't worry about the names of stages, just watch what the chromosomes are doing.

Here's a clip of mitosis in 3 dimensions. The narration is complex but the animation is good.

• Mitosis -Narrated and/or step-through animation of mitosis with a quiz at the end.
• Cells Alive - mitosis - Compare a diagram of mitosis with photographs of an actual real cell dividing.
• Mitosis and the cell cycle - Narrated animation and a quiz. Animation is nice but the text level is high.
• Mitosis and cytokinesis - Narrated animation and a quiz. Animation is nice but the text level is high.
• BBC Science: Cell division - Cell division by mitosis, including stages, and then a test.
• Mitosis: Interactive Java Tutorial - Very detailed description of mitosis, and an animation to boot. Not particularly interactive.
• Genetics Review: Mitosis - Brief diagram and text reminder of the names of the stages of mitosis for Year 13.
• Mitosis and cytokinesis - Animation of these processes in a plant cell. High level text. 
• Cell division and cancer - Extra for experts. A somewhat long but good review of cell structure including specialisation, as well as cell division by mitosis (with an animation; no stage names). Includes what happens when cell division goes out of control i.e. cancer. Self-check tests throughout. 

MEIOSIS

Best animation I have seen of the first division, but doesn't feature much detail on the second division.

• Stages of meiosis - Beautifully coloured animation with a quiz.
• Meiosis - Nice animation with stage names and controllable slider. Step-through or narrated.
• Mitosis and Meiosis Comparison 1 and Comparison 2 - Animation is the same for both, but quiz differs.
• Special features of meiosis - Shows crossing over in closer detail as well as highlights the reduction division
• Crossing over interactive - Click through the stages to see how crossing over creates new combination of alleles (using colours, rather than letters, to represent alleles)
• Random orientation of chromosomes during meiosis - Another animation of independent assortment. A pretty one.
• Independent assortment and gamete diversity - An animated and narrated or step-through tutorial and a quiz. Good coverage.

MITOSIS VS MEIOSIS: COMPARISONS

• How Cells Divide: Mitosis vs Meiosis - A brilliant side-by-side animation comparison of these two cell divisions which highlights the differences between them. Stages are named and described but can be ignored for Year 11 and 12. If the flash doesn’t work for you, try the text-only link here.
• Comparison of meiosis and mitosis - Another superb animation of meiosis vs mitosis. This one you can fast forward and rewind easily.

Year 11 The Life Cycle of Flowering Plants

Not many links collected yet, I'm afraid.

Photosynthesis and respiration - Short review of the processes and balance between them, including factors that affect photosynthesis. You can try a Test Bite at the end to check your understanding.

Flower structure - A simple interactive animation allowing you to dissect a flower and find out more about the function of each part, then practise labelling the flower. 

Pollination and fertilisation - Short animation showing the distinction between the two.

 

Food chains – producers - Stick to pages 2, 3 and 4 for “Plants and photosynthesis”; “Getting carbon dioxide, light and water” (includes leaf structures involved) and “Respiration in plants” , The rest doesn’t apply.

Plants - Photosynthesis and factors that affect it, as well as a bit on minerals. A Test Bite at the end.

Primary and secondary growth - Introduction, prequiz, animation and postquiz.

Secondary growth - Animation showing how secondary growth adds a layer of xylem cells to stem to make it wider. Quite easy to follow.

It’s a green world - Includes: Photosynthesis; Osmosis, Transport in plants (not part of your topic, but relates to what xylem and phloem do); Minerals in plants. Tests at the end of each section. 

The Poetry of Reality

Another song from Symphony of Science - about how useful science is as a tool of thought and investigation.

It features 12 scientists and science enthusiasts, including Michael Shermer, Jacob Bronowski, Carl Sagan, Neil deGrasse Tyson, Richard Dawkins, Jill Tarter, Lawrence Krauss, Richard Feynman, Brian Greene, Stephen Hawking, Carolyn Porco, and PZ Myers, promoting science through words of wisdom.

The Unbroken Thread

Here is a song produced by Symphony of Science. They take footage of and quotes from prominent scientists and set them to music  using autotune. This video about cells and evolution is called The Unbroken Thread, and features Carl Sagan, David Attenborough and Jane Goodall.

Information about rocky shore organisms

University of Otago's NZ Marine Studies Centre guide to marine species

Guide to northern NZ rocky shore species part 1 and part 2 - pictures and names only.

The rocky coast on Te Ara - the encyclopaedia of NZ.

A fungus that can break down polyurethane plastic, underwater and without oxygen, was found in an Amazonian rainforest.

Pria Anand was a student in Yale University's class of 2010 whose passion for the environment made her want to make a difference. Anand wanted to find out if there was something in nature that could decompose plastic. She began experimenting with dozens of species of fungi from the Amazon, but she graduated before she could finish her work.

Jonathan Russell took over for Anand... One day, as he casually walked into the lab he says his eyes locked on the Petri dish containing his experiment: the plastic was gone. He'd found what they'd been looking for.

The Yale students had discovered that Pestalotiopsis microspora fungus can break down plastic.
...
Today, Russell is working on his Ph.D. in molecular biology at Harvard. He's encouraged that other students are taking an interest in environmental solutions.
"Growing up in a world where pollution is going to be a big issue in the future, coming up with creative ways to tackle it, gets me excited," Russell says. "I only hope that more people will take this on and get interested in it in the future."

Parasitism

One example of a biotic factor is whether or not an organism is infected by any parasites.

Parasites are organisms that live on or in another organism, and typically cause them harm by doing things like using up their food resources, or maybe even damaging tissues and organs. As the host is harmed by the parasites, while the parasites benefit, parasitism is an example of the exploitation type of interspecific relationship.

But can parasite do more than just use up resources? Possibly. This article is about a parasite called Toxoplasma gondii, which lives for at least part of its cycle inside cats, and is egested in cat poo.  It has been observed, in studies on rats, that rats infected with T. gondii behave differently from uninfected rats: among other things, they are less fearful of cats (although not of other predators) and actively seek out areas where cats might be, through scent signals from cat urine. This would, of course, mean a rat has a much greater chance of being eaten by a cat, and thus bring the parasite back into a cat to complete its life cycle.

Humans can become infected with this parasite through handling cat poo (such as cleaning litter boxes) and not cleaning up afterwards properly, or through eating unwashed vegetables. Evidence collected so far suggests that T. gondii can also change the way our brains function, though with different effects in males compared to females. Males may become more introverted, less caring about what others think of them, and more suspicious and likely to break rules. Infected females do the opposite. One interesting (and scary) possibility is that this parasite could be the cause of schizophrenia! Maybe other parasites can explain behavioural changes often seen with some diseases. Read the article for details.

 How Your Cat Is Making You Crazy

Just another way that environment can affect phenotype.

Prejudice - Tim Minchin

A poignant (?) song that refers to how some words have significant power to express hate and to discriminate.

It's also catchy and has some fantastic rhymes, as well as a twist I won't spoil for you...

(This has absolutely nothing to do with Biology, but saves me from taking valuable class time away by playing things like this that are possibly not so appropriate. Contains swears.)

Storm - Tim Minchin

I'm not a religious person at all - I'm not even what I'd call spiritual - but that doesn't mean there isn't a lot to marvel at. As long as you're doing it with a critical mind.

You know I like to rant about various things, well, so does Tim Minchin. In this, a beat poem, he has a go at new age-y crap.

Sorry about the swears.

Fighting racism...with music!

So some chick posts a fairly racist rant, this guys sees it, and write a song to reply to her post.

It's a really nice song for starters, but even funnier when you have seen the original rant that inspired it (linked to in the video) in full .


Also, if you think the style seems familiar, but can't quite pick it, read the description below the vid. Yes, of course!