Journalistic Integrity - Is this still a thing?

This line of thought was instigated by the watching of Kill The Messenger, the brief biopic of journalist Gary Webb starring Hawkeye a.k.a. Jeremy Renner. It followed the one man against the establishment, both government and mainstream news, trying to expose a government scandal about CIA and the cocaine epidemic. Emotionally twanging human story, but it got me thinking further about what this implied about journalism. 

Now, the only thing you can walk out of a biopic and know for sure is that the actual series of events was anything but this.
But, keeping that in mind, it still calls into question the entire construct of journalism. Is it anything beyond the spread of truth and the information of the populace? Is there anything that is too true to share ?   

I don't have the first shred of expertise to examine this from a general viewpoint, but I can look at in from the narrower sub-genre of science journalism.
What is it's purpose? To inform the general public about what science is, the work that scientists do, and why it matters. 

Is/Will there be anything in science that is too true to share?  It is definitely not beyond the realm of possibility. I can already think of things that may be societally unacceptable but necessary to the advacement of humanity, like human genetic manipulation, human testing, and other politically controversial matters like embryonic stem cell therapy. Science and maybe even the populace may be better having these things, but is there ever a case where any establishment is justified in its secrecy to withold information about it's use from the public?

Well, when you put it that way...Worth a ponder.

You Won't Believe How Animals Sleep - Part 1

Sleeping kitty. 
(http://en.wikipedia.org/wiki/File:RedCat_8727.jpg)

Ahhh... Sleep.
That peaceful, restful, bliss. I don't have to tell you how nice sleep feels. You do it yourself. Just about everybody does. Not only humans, but pretty much all animals. Something resembling sleep has been documented in almost all animals, for birds to bees. If you are, like us, a wannabe scientist, you may have asked what should have been the dumbest question of them all. "Why do we sleep?". We have a few plausible theories, but first, let's look around us for a bit.

The first reality check we have to pass, is that we are a bit dumbfounded here.
All humans, since the dawn of the species, have spent almost a third of their lives in an unconcious state, sometimes vividly hallucinating (dreaming) 

Humans aren't the only ones to behave in this curious way. All mammals do it, so do birds, and bees, and cockroaches, locusts, crayfish. Also scorpions, reptiles and even insects. Every tested animal showed some variant of the process of sleep, and still, we are not much closer to knowing why.

In fact, after studying sleep in animals, we seem to have ended up with more questions than answers. 

To get a handle on what is going on during sleep, we have to go to the control room. The mother lode, the source of all behaviours and actions - the brain. With medical procedures now as advanced as they are, we can just drill a hole into an animal's skull, stick some electrodes in there, and watch what happens as it goes about it's activities, including sleeping. [1]

A dolphin, with blowhole visible. That is the quivalent of a breathing hole
(http://en.wikipedia.org/wiki/Dolphin#mediaviewer/File:Bottlenose_Dolphin_KSC04pd0178.jpg)

Now, keeping that in mind, consider the situation of a dolphin. It lives in the water, but is a air-breathing mammal, so it has to periodically come up to the surface to respire. They are also concious breathers, which means they have to conciously come up to the surface to breathe, every few minutes. Now also take into consideration the fact that a dolphin needs to sleep, often 8 hours a day. When you look at those two together, there is an obvious problem.
How does a does it stay afloat and get the air it needs to breathe while it sleeps.

Nature, as usual, when faced with difficult problems, often comes up with genius, often borderline crazy solutions.

How did it solve the problem of breathing while the brain needed to rest? Pretty simply.
It slept half a brain at a time.

Let me repeat that.

It sleeps half a brain at a time.

If you were as shocked as I was when I first learned this, you need to take a minute to think about this. This is known as uni-hermispheric sleep. This is how the dolphin solves the problem of breathing while simultaneously allowing its brain, or at least a part of it, to rest. 
Now from there outside, nothing is apparant, but, if you stick electrodes into it's skull, its clear what the dolphin brain is doing. 

The brainwaves of a patient when awake (highlighted in red) and when they are sleeping.
(http://en.wikipedia.org/wiki/File:Sleep_EEG_Stage_4.jpg)

One half of their brain, is exhibiting slow wave sleep (second half of the image), while the other hemisphere is representative of the short high-frequency waves of wakefulness.

So we've seen that all animals need to sleep, and even when they're in conditions that don't make it easy to do so, nature finds a way to circumvent the problem, and get that sleep.

Next up, in Part 2, where ducks come into the pictures, what it means for humans, and why you can't get a good first night's sleep in a hotel room.

Additional Information

This article was inspired by a segment on the radio show Radiolab (http://www.radiolab.org/story/91528-sleep/)

[1] This may seem like a horribly cruel thing to do, but in reality, these procedures aren't too invasive at all. With a few minutes of the anaesthetic wearing off, animals are back to their routine activities of eating, jumping and lazing around.

Further information about uni-hermispheric sleep:

http://en.wikipedia.org/wiki/Unihemispheric_slow-wave_sleep

Lapierre, Jennifer L.; Kosenko, Peter O.; Lyamin, Oleg I.; Kodama, Tohru; Mukhametov, Lev M.; Siegel, Jerome M. (2007). "Cortical Acetylcholine Release Is Lateralized during Asymmetrical Slow-Wave Sleep in Northern Fur Seals". The Journal of Neuroscience 27 (44): 11999–12006.

Rattenbourg, Neils C.; Amlaner, C.J.; Lima, S.L. (2000). "Behavioral, neurophysiological and evolutionary perspectives on unihemispheric sleep". Neuroscience and Biobehavioral Reviews 24 (8): 817–842. doi:10.1016/S0149-7634(00)00039-7. PMID 11118608.

Metamorphosis, And How It Is Not As Simple As You Think. [Part 1]

Metamorphosis.
noun: a change of the form or nature of a thing or person into a completely different one, by natural or supernatural means. [1]

From this graph, you can see that this concept has been around and in discussion at a fairly constant rate. The idea that an one object can turn into a very different one, is fascinating for various reasons. How does this happen? Or more importantly, why?

To answer these questions, we need to observe it in action. 
There is geological metamorphosis, where changes occur in minerals or geologic textures. It takes place due to temperature, pressure, and chemically active fluids. There is no underlying 'why', here, except that rocks that are placed in certain conditions behave in certain ways (according to the laws of physics and chemistry).
Then, there is biological metamorphosis, a completely different beast (sorry, couldn't resist). This process involves significant change in structure due cell growth and differentiation after birth/hatching. This process is so successful, that the majority of all insects (and therefore the majority of all animals) undergo some form of metamorphosis.
Let's look at this in a little more detail, in the case of the Monarch butterfly (Danaus plexippus). The monarch butterfly is part of the homometabola subclass of insects that undergo complete metamorphosis, passing through a distinct pupal stage.

Danaus plexippus start out their life as a caterpillar, hatched from a tiny egg. For around two weeks, they roam around their host plant, eating all the leaves they can find. This allows them to grow more than twenty-fold, from a length of ~ 2mm, to ~ 5 cm.
In the image below, the one on the right has just hatched, and will grow in size for around 13 days till it becomes the size of the one on the left.

https://www.math.auckland.ac.nz/~hafner/monarch/

But what comes next is what we're interested in. 
The caterpillar finds a nice spot, attaches itself to a branch, hangs underneath, and forms a pupa (also called chrysalis).
This beautiful video shows the pupation process:

And after another 2 weeks in the pupa, they emerge, as the beautiful, photogenic, Monarch Butterfy.

The Monarch Butterfly  (http://en.wikipedia.org/wiki/Monarch_butterfly)

But, wait. 

What just happened?

How did a creature go from being:

Stop reading for a moment, and think about it. How do you think this transformation happens?

Thought about it? Ok.
Scientists a few hundred years ago wanted to know too, so they took a pupa, and cut it open.

And what did they find?
Goo. 
Pale yellow goo.
Are you surprised?
There was no caterpillar, no butterfly, just a snot colored liquid. No head, no antennae, no legs. Where did the caterpillar go? 

It seems like once the caterpillar gets into it's chrysalis, it releases enzymes that dissolve it's tissues into individual cells. Some of these cells rupture, and when they do, their contents (the proteins, cytoplasm) all spill out. 

When early scientists first saw this, they came to the conclusion that the caterpillar entered the pupa, effectively died, and out of its remains was reborn as a butterfly. This explanation was used for a long time as an example by the Church to demonstrate how the human body might die, and attain a more beautiful form in heaven.

This idea was squashed completely in two different ways. The first is an ingenious experiment run by scientists in the UK. Here's what they did. They took a bunch of Manduca sexta (also called the tobacco hornworm, a species of moth) while they were in caterpillar form, sprayed them with an odor, and then shocked them (with electricity). After they did this often enough, the caterpillars learned to hate the odor, and everytime they smelt it, they tried to move away. Now, they let those caterpillars pupate. They spent two weeks in the pupa, and emerged as moths. Now, the scientists gassed them again...... they hated it! Ordinary unconditioned moths did not have any specific reaction to the odor, but these moths hated it, and kept trying to avoid it. [2]

Why? What does this mean?
It means that the memory made it through the goo.
What the caterpillar learned, the moth remembered. This conclusively proved that the caterpillar didn't die in the pupa, it simply transformed.

Another experimenter that subverted the "dying" hypothesis was a Dutch microscopist called Jan Swammerdam. He routinely performed dissections of dragonflies and mayflies and examined them under a microscope. On dissecting the caterpillar form of those insects he was able to show undeveloped structures of the adult. So on peeling back the skin of the caterpillar, you found tiny, thin wings, antennae and legs of the future adult, even before pupation began.
This proved, beyond a doubt, that the insect before pupation and after was the same organism, with shared organs.

Today, we call these immature little adult structures imaginal discs. The goo in the pupa actually contains lots of these bunches of cells, which use the nutrients spilled out of the other cells to fuel growth of those parts of the adult body.

In Part 2, we explore how metamorphosis is actually useful, why it was evolutionarity selected for, and can we see what goes on inside the chrysalis?

Sources and Further reading : 

[1] http://en.wikipedia.org/wiki/Metamorphosis
http://en.wikipedia.org/wiki/Endopterygota
http://www.scientificamerican.com/article/caterpillar-butterfly-metamorphosis-explainer/
http://www.scientificamerican.com/article/insect-metamorphosis-evolution/
http://www.radiolab.org/story/goo-and-you/

[2] http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001736

How to See Without Glasses, and Happy Pinhole Day!

Sight.
It is one of the senses that we are most reliant on to gather the information that we that we use to navigate the world around us. The spherical sacs of fluid embedded in our skulls (eyes) that give us a picture of the world, are not perfect, however. A large percentage of the human population has some form of low visual acuity (technical term for clarity of vision). We usually value our vision so much, that we are quick to correct the imperfection, with glasses, or contact lenses. But what if you don't have those with you right now, and you want to see something clearly?

Here's a little trick that will let you do exactly that.
Take off your glasses (if you have a pair) or just look at something at a distance. Look at anything that looks a little blurry. 
Now take your hand, and form a tiny little hole, like this and put it up to your eye. Do you see the difference?

This video will explain exactly how to make it, and a little bit about how it does.

Let's understand a bit more about the effect.
It is called the pinhole effect. It got its name from its usage in old cameras that didn't have lenses to focus the light onto the film. To ensure they had a clear picture, they used a hole in a board made with a pin (hence, "pinhole") as the aperture. The advantage of doing this was that they didn't need to worry about focusing on a single spot anymore.
The first of these cameras were made as far back as the 10th century AD, and the technology has developed ever since to take long exposure pictures of objects. It's utility for us lies in obtaining a clear image of an object that was not in the focal plane (technical term for everything at the same distance from the eye as the focus). This allows pinhole cameras to have an infinite depth of field (another technical term that tells you the size of the focal plane), which means everything, near and far, seems clear and focused.

Pinholes 

By allowing the light to pass through only a single point, this prevents blurriness and makes the image clearer (in an eye or a camera).
This is also why some people squint when they can't see clearly. The squinting reduces the size of the aperture (technical term for the size of the pinhole) and this makes objects less blurry.

The disadvantage is, though, that since you are blocking light rather than redirecting it, you lose a bunch of it, and your image is darker.

Lens images have more light, so are brighter than pinhole images.

So now you may want to build your own pinhole camera, and here are some helpful intructions on how to do just that.

And lastly, today (27th April, 2014) is actually World Pinhole Day. Congratulations!

Here are some more images of pinhole photography, along with information about World Pinhole Day. (http://www.bbc.com/news/in-pictures-22150973)

Schools need to teach debugging

Debugging. 

The process of finding and remedying errors in a design. Can apply to code, circuits, projects, whatever. 
The Art of Problem Solving.

Why is this important?
We have problems everywhere. No one produces flawless material time after time. Sooner or later, you're going to make a mistake. It's basic math. Your success rate is a probability variable, taking values from (0<=c<1) [Can't be 1, because perfection is a physical impossibility]. The longer you go without making a mistake, the more likely you are to make one.
So everyone will come across problems. So they need to be taught how to deal with those problems. Ideally, school should do this. Schools exist to teach. They try to teach a whole variety of things from Sissytory, no Borography. But they don't seem to teach something that everyone will need, sooner or later.

And the longer they go without making a mistake, the harder it hits when the point finally comes.

Other people think this too.

Source: http://danluu.com/teach-debugging/