Evolutionary Biology: Recent Highlights

Sometimes I forget that Fresh Brainz is supposed to be some sort of science blog.

Truth be told, that part is easy to forget. It's tough to write anything fun about serious science since 99% of the original research that I read is about as exciting as watching mud dry.

In slow motion.

Luckily for humanity* there is still some cool science out there that must be highlighted in this blog!

Here are three of the finest findings in evolutionary biology so far this year:

1. Planet of the Apes. Now with Spears.

Human beings have been killing each other (and small defenseless animals) with evil, sharp implements for so long that we believed no other animal can do it.

Actually they just don't want to do it, being the nice, peaceful animals that they are.

They'd much rather puncture your juicy jugular with their amiable teeth and slash your abdomen open with their friendly claws.

However, a group of researchers have noticed that some chimpanzees in Senegal prefer to hunt their prey using sharpened sticks, just like early humans.

Scientists already know that chimpanzees can use tools for a number of years; the chief novelty of this study is the detailed observation of the tool sharpening process.

Which actually involve the use of teeth.

Now that chimpanzees have learnt how to use spears to hunt, we should all shudder in fear of ... "Death by Britney"!

Seriously, we've all had enough of that Spears.

Click here to read more.

2. Mice with Better Colour Vision than Some People.

The worst enemy of most people is some people. Some people rob. Some people kill. Some people like country music.

Some people write science blogs.

In addition, some people are red-green colour blind. Mice are also red-green colour blind because they lack a type of photo receptor that are found in the eyes of most people.

When researchers inserted the human gene for this receptor into mice, the genetically modified mice could now distinguish the difference between red and green much better than regular mice.

This demonstrates that the mammalian brain already has sufficient flexibility to adapt to modular changes in colour vision. You don't need to change a large number of genes and rewire the whole brain to allow the mice to benefit from this enhancement.

Just one gene will do.

Another nail in the coffin for Irreducible Complexity.

Check out more details here.

3. Do Dinosaurs Taste Like Chicken?

Why does everything taste like chicken?

Is existence merely a massive game of virtual reality where powerful supercomputers manipulate the lives of millions of innocent victims?

But enough complaining about taxes.

Scientists have successfully isolated protein fragments from the inside of a 68 million-year-old T. Rex bone uncovered in Montana, USA. They sequenced these fragments and found that it resembles a similar protein found in modern chickens.

Direct molecular evidence of the close evolutionary relationship between dinosaurs and birds.

The principal investigator of this study, Prof. John "Jack" Horner actually mentioned the project last year when he came to Singapore during a dinosaur exhibition. So I am happy to see that they have produced spectacular results in such a short time.

More stuff can be found here.


Would you like to know more?

About other forms of fun research:
- Boob Physics

*The term "humanity" includes all Fresh Brainz readers, most dolphins and some bonobos. It excludes most other human beings (especially Brad Pitt) and any talking cats.

Impossible Quiz

A new Flash game is sweeping through the bioscience community and wiping out any semblance of productivity this week.

It's called "The Impossible Quiz".












No, it's not really impossible but it's filled with such twisted humour and bizarre logic that Fresh Brainz feels right at home with this cruel-joke-masquerading-as-a-puzzle-game.

For the want of a shoe, my friends.

True.


Would you like to know more?

About other people with a sick sense of humour:
- Tom Weller
- Brainiac
- Despair Inc.

Face Transformer

Just found this impressive online toy that morphs a photo of your face into a number of interesting variations.

Oooh I love gadgets! So I went right ahead and submitted my own mug.

Here are some of the results:















It's obvious that whichever ethnicity or even species that I morph into, the geekiness still shines through. *sigh*

This certainly isn't the first online face morphing tool, but I must say that the results are surprisingly plausible. The application was designed by a research group at the University of St. Andrews in Scotland, so perhaps that's the reason why the output looks professional. People are getting really good at doing this.

Click Face Transformer to go there and submit your own photo (or the photos of your enemies).

It's a simple two-step process to produce a morphed photo.

So, which are my favourite results?















That's me in the year 2047. I know many of you ladies would rather not know how you will look like in 40 years, but this was the first result I selected - and I quite like it actually. Despite the wrinkles and spots, my elder self has a look of serenity and contentment that is missing in the 2007 original. I hope I actually look as wise and at peace by that time.















I also like the Manga version of me, with the big nerdy glasses and awkward smile. Almost looks like an engineering student who has a such a pure heart that a bunch of horny goddesses would fight over him at school.

Oh my fantasy!


Would you like to know more?

About other gadgets:
- Calculate your nerdiness!
- Pop-up photos!

About other goddesses:
- Olivia Newton-John (Terpsichore)

Audio Cassettes: Simplest Explanation of Cancer

Just a couple of weeks back I found a drawer full of old audio cassettes containing pop songs from the 1980's and early 90's.

I was thinking of recording some of this music into MP3 format, since the magnetic tapes in these cassettes have been deteriorating so badly. One inconvenience of living in the tropics is that fungi tends to grow on all sorts of stuff.

For some reason they really like to eat magnetic media and optical surfaces. Video cassettes have it the worst - they are usually unreadable after only one year. We didn't have one of those expensive dry cabinets so some of our cassette tapes have endured the humid environment for decades.

As I was saying, I wanted to find out how many of these tapes are still readable, so I went out to buy a new cassette player (these are nearly extinct nowadays amidst the truckloads of MP3/MP4 players) and took a listen.

Sure enough, the newer cassettes were still fine, but the condition of 20-year-old tapes was much less consistent.

Some were only readable for a few songs, and the rest sounded muffled. Others were a scratchy mess throughout. Most of these old tapes clogged up my player's magnetic head with rust and fungal gunk after a few songs. All of them showed their age.

In contrast, all the CDs I bought still sound like new, including my first CD - the "Empire Strikes Back" soundtrack - which is 15 years old.

Ah, the wonders of digital technology!

Wait. That suddenly makes me think of something.

Fresh Brainz is proud to bring you the simplest explanation of cancer in the blogosphere - using audio cassettes as an illustrative analogy!* (see footnote).

Imagine you have an audio tape full of your favourite songs.















Magnetic tape is similar to a DNA molecule in a number of ways:

1. They require physical contact to be read and copied.
2. The analog copying process is imperfect and successive copying will lead to information alteration or loss.
3. They are both subject to wear and tear over time.
4. They have two anti-parallel streams of information. In DNA these two streams are complementary, whereas in an audio tape they usually encode two different streams (Side A and Side B).

Let's assume that you have recorded the same set of songs on both sides of the tape.

You love those songs so you play them everyday.

Now for the challenge...

How would you make your songs last 20 years?


















Well, you could maintain the original cassette as carefully as you can.

Unfortunately, you need to use it everyday, so the tape is subject to constant wear and tear. Environmental effects like background magnetism, humidity or static electricity will also degrade the signal.

Thus, you will need to check the cassette regularly to see if your songs still sound the same. Luckily you have the same songs on both sides, so any one problem is unlikely to happen to the same part of the both songs. You can use an audio editing machine to copy an intact song on one side and overwrite the damaged song on the other side.

This situation also occurs in living cells. DNA repair mechanisms use one strand as the template to repair the other.

Unfortunately, this is a lot of work that takes up time and energy. Constant editing and overwriting makes your cassette age quickly. Similarly, continuous DNA repair work is exhausting for individuals cells and they grow old fast.

Moreover, the rest of the cassette is growing old anyway. The case can crack, tape can get torn off the spools - you might even accidentally drop the whole thing into a river one day.

It isn't safe to put all your eggs into the same old, rusty basket.

















So, why not make copies of the original cassette? Before it gets worn out, transfer the music to a fresh new cassette. Simply repeat this cycle and voila! You will have songs that remain forever new.

This will work for digital files, but unfortunately for audio tapes and genomes, the copying process (replication) is not perfect. Analog tape duplication introduces artefacts such as reduced signal intensity, increased noise, wow, flutter and others. Similarly, DNA replication (using polymerases) has an error rate of at least one base pair per million, usually more.

The result: successive copying adds more and more errors to the songs. In a cassette tape the final product is poor quality music; in the DNA of a living cell, the replication error may end up in critical parts of the genome (shown as red sections in the diagram) that causes the cell to divide uncontrollably.

Which leads to cancer.

However, constant cell division is necessary to keep the multicellular organism young. Even if a cassette tape gets destroyed (shown as a red "X") the music still survives. Thus there is tug of war going on between DNA repair and replication.

If I must summarise the opposing forces that a cell must manage into a single statement (yes, it is an oversimplification), it would be:

Young and Restless -vs - Stable and Dying

A cell would rather be young and restless, because it doesn't mind the replication errors that turns it into a super reproductive machine. It hates spending excess energy on DNA repair, because that makes it old and grey. Cells are good at dividing and lousy at dying - this must necessarily be true, otherwise we wouldn't be around.

However, with the exception of certain cell types (such as reproductive cells), the entire organism would rather its cells be stable and dying, because an aggressively spreading tumour will destroy the whole system much faster than the slow ageing process.

I think it is curious that complex multicellular organisms contain a number of such features that are beneficial but yet destructive at the same time.

Living systems can be functionally superb, but no existing species can possibly be perfect because, why, perfection tends to take a long long long time.


Would you like to know more?

- Prof. Jarle Breivik (University of Oslo, Norway) has an informative homepage and a link to an easy-to-read Scientific American article about evolution and cancer.

*Footnote

I made up these definitions a while ago. Illustration by analogy is always inaccurate, but due to its simplicity and clarity, it is still a popular communication tool today.

Explanatory Analogy - This type of analogy so closely parallels the problem of interest that it can provide explanations and predict results. For example, some Gedanken experiments in Physics use explanatory analogies.

Illustrative Analogy - This type of analogy is similar to the problem of interest in only a few ways and is simply used to provide a clearer mental picture for communication purposes.

The Lonesome Science Blog

My BlogPatrol account informs me without much fanfare (actually no fanfare) that Fresh Brainz has just seen its 10 000th unique visitor since September 2006.

A big thanks to all Fresh Brainz readers!

*bows*

While reaching this important milestone is encouraging, I've observed something that is making me rather worried.

In the nine months since the inception of Fresh Brainz, the total number of blogs tracked by Technorati has gone up from about 50 million to an astonishing 79.2 million today.

Yet the total number of Singaporean science blogs remain at two.

The only other Singaporean science blog I know of is The Biology Refugia.

The Singaporean blogosphere isn't dying you know.

It's growing every day. Last I checked there were a few hundred thousand blogs.

Of which two are about science.

Despite the millions of dollars spent and thousands of new researchers engaged in this nascent endeavour.

Hmm.