Friday, February 29, 2008

What if your drawings came alive?

Now this is really cool- could this be the 'killer app' tablet PC's have been waiting for?

Sunday, February 24, 2008

The Evil Virus that Lives Inside Me
To paraphrase Khalil Gibran (aka "The Prophet"): Our genomes are not really our genomes- they come through us, but not from us.

Our genomes are not even all 'human' - about 8% is 'virus scar' - otherwise known as HERV's "Human Endogenous Retroviruses". This DNA got there (for example) when an HIV-like virus infected the ovaries of a little squirrel-like creature a few hundred million years ago. That squirrel evolved into me, you and everyone we know.

Once this viral DNA gets in, it doesn't just stay put- it stamps itself all over the genome, making thousands of copies of itself and buggering up lots of other stuff. Like a badly graffitied library book - sometimes the meaning of the text is lost or changed.

Most of this viral DNA is just fossilized "junk"- but some (previously) viral genes have been coopted by our cells to make placentas- they allow the fusion of primitive placental cells known as "trophoblasts". Unfortunately, some also seem to be pretty good at helping good cells turn into invasive cancers.

Over the aeons, the viral DNA has become dilapidated- degraded by mutation. The genes that normally allow a HERV virus to escape from a cell are now defunct. These antique viruses are therfore trapped inside us- unable to escape and become infectious particles.

That is until 2007 when some guys decided to re-create an infectious version of HERV-K : a virus whose last outbreak was over a million years ago.

An extinct human pathogen- dormant but surviving in a crippled state through geological timescales is resurrected. We have no immunity. Bang! it's the end of the world (yet again).

What happened to "ethics committees"? Hasn't anyone read Greg Bear's novel "Darwin's Radio"?

Leslie Feist: 1-2-3-4

Leslie Feist is great... seeing her next week. The "i'm suffering from sinus" look doesn't do her justice- she looks like the woman in the anti-histamine ad pre/post dose.

Saturday, February 23, 2008

Shaved and Horny : Myostatin Revisited

A while ago i blogged about myostatin- a gene that inhibits muscle growth. When the gene is defective, muscle growth continues unabated. Here's a National Geographic video about it- with particular reference to the "double muscled" Belgian Blue cow. The interviewer is clearly an idiot - "does that mean they have two of every muscle?".

Note the muscle tremors - "myoclonus". Why isn't PETA outraged? Because these cows were "bred" the old fashioned way.

It's reminiscent of the furore over GM Canola. The fact is Canola has already been "Gee-Emmed".

Canola used to be green, bitter, smelly and (to top it off) contained a potential cardiotoxin. After bombardment with mutating X-rays and a bit of artificial selection- bingo! - toxin eliminated. Of course the old moniker "rapeseed oil" had to be ditched - "Canola" comes from the term "Canadian Oil, Low Acid".

Synopsis: Test tube or selective breeding? - It doesn't matter how an animal (or plant ) has been "genetically modified"- what matters is how freaky it ends up being. I think we should ban the Belgian Blue, and while we're at it - these ugly dogs. Any other suggestions?

Friday, February 22, 2008

Tuesday, February 19, 2008

There's a Photo of You on the Moon Too!!!

In the 70's some astronaut left a family portrait on the moon. How cool would it be knowing that , whenever you looked up at the moon at night, there'd be a picture of you there looking back. Seriously cool.

Some company is now offering me (and you) this same 'once in a lifetime' chance. ... only this time it'll be a digital image of your family, along with ten trillion other strings of zeros and ones. And there not really even zeros OR ones- there just a long string of things that can be in one state or another- magnetic fields, pits in disc. Lets say it's a DVD or a Blu-Ray (kudos Sony) disc that gets dumped on the moon. Let's not consider it littering.

How cool would it NOT be -knowing that whenever you looked up at the moon at night, there'd be a series of microscopic pits in a disc that correspond to your family? Hmmm.

When i say 'correspond'- you'll of course need to know what format the image is in to actually decode it. Will it matter to you if it is a JPEG, a TIFF or a BMP? It should do- because that list of binary digits will need to be completely different. Otherwise it'll be like being a blind kid whose astronaut father leaves a photo on the moon: if you've never seen a photo, and never seen the moon- imagining both together is probably going to leave you less than satisfied.

Here's what i propose instead of all this- and it doesn't involve littering:

Since it is both the data and the format algorithm that TOGETHER generate 'meaning'.... why not use data that's already on the surface of the moon? Lets say you generate a long list of numbers that correspond to all the craters' diameters, longitude and latitude. You then convert these into a very long series of zeros and ones (or elephants and telephones).

Then, you hire an earthbound mathematician, and tell him to think up a complex equation, 'format' or algorithm that will convert your new data set into a beautiful 8 x 6 color portrait of your family.

Viola! There's a photo of you on the moon- and there always was.

OK- so there's also the complete works of Shakespeare and all your ex-girlfriends' telephone numbers- but that's not the point.

Monday, February 18, 2008

Syndromes 3: of Cyclops and Skin Cancer!Sonic_hedgehog_pathway.pngCorn Lily, False Hellebore (Veratrum californicum)Chemical structure of cyclopamine the Cyclops.

Gorlin's syndrome patients can have enormous numbers of skin cancers known as BCC's - "Basal Cell Carcinomas". They also have characteristically widely-spaced eyes (hypertelorism)- along with numerous onther problems including palmar pits, jaw cysts, splayed ribs etc.

The syndrome is due to a mutation in a gene known as PTCH. This codes for a receptor that binds a protein that is critical for embryonal development. This particular protein has the unusual name of "Sonic Hedgehog" - named after the Sega video game character! (If you discover something, you get to name it).(see red sqiggle in diagram above).

Too much activity of "Hedgehog" and you get the widely spaced eyes and skin cancer of Gorlin's syndrome- BUT too little and you get to be a "Cyclops" - at least for a few months of gestation.

Following investigation of a number of cyclopic calfs in Idaho in the 60's, it was discovered that the cows had been grazing on a native weed containing a teratogenic alkaloid - now known as Cyclopamine.

Some bright sparks are now rubbing it into skin cancers- but not those on pregnant women.

Syndromes 2: Blue Ears & Eyes

Alkaptonuria. This recessive condition affects one in a quarter million people- and makes their ears and eyes slowly turn blue. Sweat is dark brown, and so is ear-wax!

Interestingly the urine starts off as a normal color, but after a few hours exposed to the air it turns brown. Many cases are diagnosed in infancy with dark brown staining of their diapers.

Unfortunately, it is not all fun and games. Tendons, ligaments and heart valves also become pigmented- then calcified- causing severe arthritis and heart valve blockages.

Similar pigmentation can occur with the cardiac drug Amiodarone and the antibiotic Minocycline.

Syndromes 1: Uncombable Hair Syndrome

Dermatology - SCALP: uncombable hair

I went to watch my daughter's swimming lesson today, and saw a kid at the pool who i'm SURE has "uncombable hair syndrome"- and no, i did not take a photo of him- that would be creepy. The condition is also known as "pili trianguli et canaliculi" - the hair shafts are triangular and grooved. Most children are otherwise normal. In a related event- i bought a comb for the 1st time in my life. Every time i use it i think about my Grandfather combing his neat straight grey hair.


Rankin -> Special Projects-> EyeScapes. (Warning: "Sexy Sofa" is pretty sexy).

Sunday, February 17, 2008

Into the Wild

Ok - you'd better stop reading fast because there's a 'spoiler' at the end of this line----> He DIES! surprise.

Here's the synopsis of "Into the Wild"- based on the true story of Christopher McCandless: a young middle class suburban guy who reads too much Thoreau decides to go AWAL to piss off his annoying parents. He doesn't call, he doesn't write.

After hitchhiking for a year or two- he ends up in Alaska- and dies of starvation in a decrepit bus. Had he bothered to take a map with him, he could have found his way out from the Wild that had eventually "trapped" him- by walking 5 miles upriver to a bridge. A pointless and unnecessary death becomes a Holywood movie (via a book). A loser becomes a posthumous hero.

Sean Penn's movie treats him as a christlike figure- transforming the lives of people he meets, and ascending into heaven with a big smile at the end. Penn has made a few mistakes in his life- like marrying Madonna- and i guess this was just another one.

A MUCH better film along the same lines was Gus Van Sant's "Gerry"- Matt Damon and Casey Affleck (Brother of Ben) get lost in the desert and die of dehydration. Why better? Well, it doesn't take as long to die of dehydration so the film was a lot shorter than this 3 hour marathon. This film is also based on real life events.

The stupidity of these two is much more obvious- and (spoiler again) there's a bit of action at the end when one strangles the other (can't recall which) to save his friend from a slow agonising death. Turns out there was a major highway just over the next hill!

Tuesday, February 05, 2008

The Evil Twin that Lives Inside Me

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Your genome is like your genetic 'fingerprint' - everyone's is individual. But it's not really that simple.

Each of your cells contains hundreds of mitochondria that produce energy needed to power it. These started off about 4 billion years ago as free-living bacteria that got eaten but not digested by one of our single-celled ancestors. They have their own DNA - and thus their very own genome. (although some of these genes have jumped over to the nuclear chromosomes). This genome is also technically "yours" ... in this case it is passed down solely along the maternal lineage as sperm don't donate the father's miochondria to the fertilized egg. All of us have "Eve's" mitochondria that's been slowly mutating down the aeons.

In some cells of your body, the genome has been mixed around- some bits deleted, rearranged. The white blood lymphocytes that make antibodies (B cells) do this as they mature in your bone marrow. In this way, your body can manufacture zillions of different types of antibody than otherwise would be possible. The genome in one of your B cells is probably different to the genome in your liver or skin.

Here's where it gets more interesting: When you were a fetus, some of your stem cells managed to get into your mother's circulation- and vice versa. It's now been shown that these can survive at least 38 years! It's also theoretically possible that some of these cells could find their way into the circulation of your younger siblings. If you're a woman, it's even possible that your body contains your mother's genome, your grandmother's genome etc etc. - along with those of all your children.

This situation is known as micro-chimerism.. where there exists a relatively tiny amount of non-self DNA. It may explain some auto-immune disorders. I wonder if children born of 3 parents (sperm, egg, surrogate mother) will be shown to have any immunological differences given the (usual) complete genomic dissimilarity between the surrogate mother and the offspring. Who knows- maybe it might trigger autoimmune disease in the surrogate.

Pediatric dermatologists are often confronted by children born with unusual variations in their skin. Sometimes, there can be too much pigment or not enough, too many blood vessels or too few, too many hairs or too few. There are even conditions that cause acne in certain areas but not others.

The patterning of these changes is often described as streaky, whorled or marbled. It is presumed that they follow the lines of embryonic skin development ("Blashko's lines) and are thus termed "Blashkoid". The idea is that there is an error in cell division in one of the fetus' skin stem cells leading to two genomically distinct populations.

My feeling is that this probably happens all the time - but that most genetic changes are 'invisible' to dermatologists. It's only when the color changes that the condition becomes noticeable.

But- (this is REALLY COOL) it is also possible for 2 non-identical twin embryos to fuse together to form a single individual made of two distinct genomes. (A tetragametic chimera). Actually this sort of thing happens in marmoset monkeys all the time (see video below).

When a male & female embryo fuse, the results can be obvious at birth with a form of true hermaphroditism- both ova and testes present.

When 2 twin sister embryos fuse - or 2 twin brothers- you might never know- perhaps it happened to you. Your skin might show subtle whorls of differential pigmentation.

If you're a woman having fertility treatment and they put 2 embryo's in but only 1 comes out.... maybe you should check they haven't fused!

There are 2 situations where you might find out by accident: custody battles and organ transplant workups.

There has even been a case of fusion on an unfertilized ova, with an embryo forming a chimera of a child and (half) his own mother! (a trigametic chimera)

Monday, February 04, 2008

Jenny Lewis Again

Those "Watson Twins" are one sexy girl!

"Gravity Waves Goodbye" or "Scatological Eschatology".

In the following analogy my brain is compared to a goose, my high-school exam results are fois gras, and physics is the 'gavage'. Now read on!

When i was at high school being force-fed dry physics equations -( Newton's laws etc) i remember thinking : "..but what actually is gravity"?

The equations i learned described how things moved but i wanted to know what gravity actually was. What ACTUALLY IS IT? How is it possible that I (by this I i mean my body not my 'spirit')- that i am connected to EVERY OTHER THING in the observable universe?

The billions of trillions of stars in the night sky tug me upwards WHILST those on the daytime side of the earth pull me downwards. "Here i am stuck in the middle with you". I wonder if it is possible to estimate the total pull of all that stuff up there- what's the gravitational attraction of half the universe from here? It's pretty far away but there is an awful lot of it. (Please forward this blog entry to anyone with a physics degree).

I am attracted to my cat, your cat, your brother's cat,you and your children, that pen that you dropped in the car that slid between the door and the seat- right now i am exerting a force over that pen that reduces by the square of the distance between it and me.

Why does nobody else seem to find this utterly incredible? If it was discovered yesterday it would all over the papers. But no- it's Britney, Britney, Britney, Britney, Heath.

Honestly, even the serious "news" is a glorified version of "he said this, she said that". Nobody will remember presidents or pop-stars in a thousand years. Nobody will care who said what to who(m?) - but humanity will ALWAYS remember Einstein and Newton and that other guy i can't remember- what's him name.. Laplace? Kepler? Something.

They will be remembered as (to paraphrase Newton) the giants who have an infinite regress of mini-giants standing on their shoulders so as to see further (it's giants all the way down by the way).

Unless you are a scientist (and i don't mean a medical doctor) you should consider yourself a support network for the smart people. I am here in case there's a local Einstein with a rash. Britney exists to entertain the scientist with her heartfelt passionate music in his/her time away from the lab.

Nobody will remember us- not even our own family after 3 generations. That's all the fame we've got to look forward to.
"Granny- who is that JPEG of?"
"Oh, that was my great grandfather... he lived at the turn of the century when blogging had just been invented.".

I was told "just learn the equations". So I stopped asking questions and got 91% in physics which got me into medical school. After decades of thinking about it i still don't really get it. Maybe nobody before Einstein got it... and it probably came to him in a flash whilst daydreaming between patents. (i daydream between patients but just get more and more confused). The internet isn't helping.

It seems it's often the most obvious things that take the longest to get 'discovered' by science - think about the discovery of "air", "sleep", "consciousness". What about 'plate tectonics'? .. it's pretty clear to a 3 year old looking at a map that the continents fit together like a jigsaw puzzle- yet it took till 1960 for that theory to be generally accepted.

Ok... so don't think of gravity as a "force" between two objects. Think (apparently) about a bowling ball on a trampoline. In this case, the 3-D universe is represented by the 2-D surface of the trampoline. When placed gently upon it's surface, a bowling ball indents it.

The more mass an object has, the more it warps the fabric (of trampoline spacetime). When you place a tennis ball at the edge of the trampoline, it rolls downhill until it hits the bowling ball-(or might orbit it a bit until friction slows it down). Viewed from above, it would seem like the bowling ball is attracting the tennis ball by some mysterious force. (Bowlingballation).

More interestingly, imagine throwing a bowling ball on to the surface- you can imagine ripples in the trampoline spreading outwards from the epicentre like ripples on a pond.

These waves are analagous to "gravitational waves". They are waves of space that alternately shrink and stretch space and everything in it. A wave like this passing through a round ball - or even a drawing of a circle - would stretch it back and forth. Gravity wave detectors all over the world are poised waiting to detect this wobble.

Even more interestingly, gravity waves radiate energy away from the objects that emit them... i guess this is like vacuum friction!

N.B. "gravity" the not the same thing as a "gravity wave". A massive stationary object still exerts a force of 'gravity' but does not emit any gravity waves. Gravity is a static warping of spacetime- a Gravity wave propagates this warp.. i think.

Gravity itself also travels at "the speed of light".. although it could also be said that light travels at the speed of gravity. Whatever it is, it is the cosmic speed limit- nothing can ever travel faster.

What this means is that if the sun suddenly disappeared, the earth would continue nicely on it's elliptical orbit for eight whole minutes before the lack of gravity 'registered' and we were flung out into space. (The light would go off at the same time.).

When i first read about this, i couldn't stop thinking about it. What if it had already happened 7.5 minutes ago? Presumably, we could live in the dark burning fossil fuels for a bit- but my guess is the planet's temperature would drop within a few hours to freeze everything solid.

I guess these morbid eschatological thoughts of mine (see "The End of the World") are the atheist analogy to thinking about death and "hell". My scatological eschatological thoughts entail thinking about "Fucking Hell".

This excellent, informative video explains it all: