A Schooner of Science

Connecting via common ancestors and Genographics – Interview with Wolfgang Haak

// December 8th, 2010 // No Comments » // Recent Research, Science Communication

At the Genographic Event at the RiAus I also interviewed Dr Wolfgang Haak, who spoke about Y-chromosome markers to determine paternal ancestry. He’s been involved in the Genographic Project for three and a half years.

What are the benefits of understanding ancestry?

It’s pretty much a personal thing, at the end of the day, because I suppose everyone’s interested in his or her own genetic history. This is my personal driving force, finding out more about myself. Where’s my place in this planet, in this world, where do I tie into the global picture? That’s a big motivation for me, and as I find out more as I work with people that it’s the same motor or driving force with them as well.

We share a common ancestry after all, there’s a common interest in our genetic history as well.

What first attracted you to the Genographic Project?

I have always been interested in genetics, but I actually come from an anthropologic background and genetics is certainly a part of that. I also come from an Ancient DNA lab. This was a step further into more modern population genetics. This is about getting both things together. Having a modern day perspective, plus adding a timely depth to that picture that we get from modern day diversity.

Tell us about your own ancestry, have you genotyped yourself?

Yes, I’ve done both. Mitochondrial, I’m haplogroup H, and I can further pin that down to group H1, so that is a Palaeolithic, Mesolithic one that might have come into Europe prior to the last glacial maximum, around modern day Spain or Italy or even a South Eastern refuge. It’s not entirely clear but we’ll find out over the next couple of years.

On the paternal side its even more enigmatic. I’m part of a North African lineage that probably originated around the Horn of Africa, so there’s that connection on the Eastern side of Africa where it connects to Saudi Arabia, and that has a high frequency there into the Nile Valley, and from it spreads into South Eastern Europe. Not entirely sure when it spread across the Mediterranean region, but probably historic times rather than prehistoric times.

Genographics, Neanderthals and Cannibalism, an Interview with Carles Lalueza-Fox

// December 8th, 2010 // 1 Comment » // Recent Research, Science Communication, Sex and Reproduction

After the event last night about the worldwide Genographic Project, I caught up with Prof Dr Carles Lalueza‑Fox, the first speaker on the night, for a quick interview. He’s an expert on Neanderthals, or Neandertals I think we call them now. Named after the Neander Valley where the first specimen was discovered.

What first sparked your interest in studying Neandertals?

When the first Neandertal sequence was retrieved in 1997 I had been working on ancient DNA for a while, but then Neandertals seemed to be something in a different league.

In the first ten years it was only possible to get mitochondrial DNA from Neandertals.

For me, I really liked Neandertals and human evolution as a child. Ancient DNA was something particularly difficult at the time, and the thing that brought me to the subject.

How human do you think Neandertals were?

How human?

Yes, tricky question.

Haha, yes. It’s a very long question, a very difficult question. One must always take into mind our tendencies are always fluctuating. We saw them as a very primitive human lineage in the early 20th Century, but I’d say that now we’re turning to the point where we see them as very similar to us.

Maybe the best thing to think about Neandertals is they are more different from us than any modern human to any other modern human. That’s the way we should think about them.

If we want to think of them as a different species that’s fine for me, but there is a range of difference between us and the Neandertals.

The cuts found along Neandertal bones you suggest are evidence for cannibalism. Could they just be an example of de-fleshing prior to burial?

Well, yeah, it might be right in some circumstances. But this is not only cutting, you know de-fleshing the bones. It’s also fragmenting the bones with small stone tools, very small fragments, and even the skull, and the faces. For me it’s very difficult to think that this kind of post mortem activity is something more because this is a complete destruction of the bones.

It’s very similar to what we see in other sites with fauna, the bones are broken to extract the marrow in the same way.

And it’s a pretty common thing, well, not common these days, but certainly we humans have our own history of cannibalism.

Yes, well there are several sites with the signs in Neandertals. But you almost think that life was very tough and they were structured in very small groups, so the fact that you find another one… I mean you’d say “hey, we are Neandertals all of us,” but I’d say that’s a modern conception.

Whereas for them it might be “hey, you’re not one of my family I may as well eat you.”

Yeah, the idea of humankind, in fact, is very recent. After the second World War, and the UNESCO thing. So even the idea of humankind is more recent than we might think now.

And what do you think of the possibility of Neandertals and humans mating?

I think it’s plausible with the data we have. It was probably something that was a minority, restricted in time and space, it was nothing important in my view. The thing is we can detect it now in non-African modern humans is because this was an expanding population, so even a small event of just a few, say it was, this was amplified later on.

The Genographic Project in Adelaide

// December 8th, 2010 // No Comments » // Science Communication

The Genographic Project in Adelaide

Last night I was lucky enough to attend the Genographic Project event at the RiAus, where they discussed results of samples collected from the Adelaide public.

The event was a huge success. Every seat was full, and I was fortunate to find a spot tucked in a corner. And that despite the torrential rain that hit earlier in the afternoon, blocking traffic around the city.

One thing that really struck me about the night was the feeling of connection. The billions of humans around today arose from small populations 50,000 years ago. If you start looking back far enough, you share the same ancestral group as the stranger sitting three rows down. In a sense we’re all brothers and sisters.

As more people become involved in the project, we find out more about where and when different groups migrated around the globe. Being involved makes you a piece of the puzzle that will uncover our stories, which have been lost to the past.

Ten years since the Human Genome Project

// June 26th, 2010 // 2 Comments » // How Things Work

Image credit: Russ London

This picture is a printout of the human genome in a series of books in London. The 3.4 billion units of DNA code are in more than a hundred volumes, each a thousand pages, in type so small it’s hardly legible. That’s some good reading.

The human genome project was pretty exciting science, hell it still is. A few years ago they thought it would revolutionise medicine, cure cancer, save the world.

It hasn’t been that simple. After all, the amount of DNA we have in common with apes and fruit flies is pretty astounding, knowing the code is not enough. The way the code is read is also crucial, and we don’t understand that very well.

One thing that always interested me was epigenetics, which are non-DNA-coded inherited traits which are passed on through generations. For example how DNA is packaged in the cell determines which parts of the code are read and which are ignored. A heart cell has the same DNA as a hair follicle, but because of epigenetics we don’t have hairy hearts, or hearty heads.

Part of what the human genome project revealed was how little we know about DNA, and how many mysteries are still wrapped up inside us. Nonetheless it was one of the most important projects in human scientific history, and to that let us drink rum!

Meet telomerase, the enzyme that won a Nobel Prize

// February 18th, 2010 // 20 Comments » // Recent Research

As a pirate I am rarely afforded the luxury of meeting the rich and famous, but today I met Elizabeth Blackburn. She was awarded the 2009 Nobel Prize in Physiology or Medicine, making her the first first FEMALE Australian born scientist to win a Nobel Prize. (I also met the PM and Senator Kim Carr, just to round out my VIP day.)

Sadly the story didn’t make the news on TV… further evidence that science just doesn’t rate to the media.

Well, it rates to ME. So I’m dedicating this post to the research that nabbed the Nobel Prize, the discovery of telomerase, builder of telomeres, protector of chromosomes.

WTF is a telomere? Inside your cell you have 46 chromosomes, long strands of DNA that have ends. Chromosomes have telomeres for the same reason we shipfolk dip the ends of rope in wax – so the ends don’t fray. Instead of wax, we have the same sequence of DNA bases (TTAGGG) that repeat over and over and wrap around some special proteins to make a nice neat little end.

When it comes to that special time in a cells life when the mommy cell loves itself very much, it needs to make a copy of all its DNA so it can split into two new cells. Because of how the machinery works it needs some DNA at to hold onto before it can start copying, which means some DNA at each end is lost every time the cell splits. That’s another good reason to have telomeres, you can lose a bit of them each time and it doesn’t hurt your genes.

However you’ve only got a certain amount of telomeres, and once they run out two things can happen. One: the cell stops dividing. Two: Something bad.

Something bad is that the cell, keeps dividing and starts cutting into the rest of its DNA. Suddenly you have lose ends of DNA whipping around the cell like untied ropes in a storm. The cell freaks out and thinks “eep, my DNA strand has been cut! Must sew it back together!” and then attaches one end to another end, probably to another chromosome altogether. That’s actually okay, until it comes time to divide again. The chromosomes need to separate so they can go into the daughter cells, and oh noes they are attached to each other! Solution? Rip them apart, then sew two bits back together… somewhere… Oh dear…

Soon you have DNA that has been stitched together a bit like Frankenstein’s monster. Most of the cells will die (for obvious reasons), but some will survive, will become stronger, better, faster than before, will become the cancer.

So telomeres protect your cells, but usually run out over the life of the cell. Fortunately there’s an enzyme that makes more of those TTAGGG repeats, so you have more telomeres! That’s what Elizabeth Blackburn helped discover – the superdooper trooper enzyme TELOMERASE.

Most of your cells don’t make telomerase, but stem cells do – that’s why they can survive for your whole life. Having an active version of telomerase can help protect against that split/stitch cycle and prevent cancer forming… mice often have more telomerase in their cells, and longer telomeres – as a result they get different kinds of cancers to us.

Pretty nifty enzyme, hey. Don’t know why the media wouldn’t be interested in that… you know, protects against cancer, important part of stem cells… no, don’t put THAT on the news. Let’s have some hardcore sport and a weather feature or two. GORDAMMIT!!!

DNA dating websites – the genetics of love

// February 5th, 2010 // 3 Comments » // Just for Fun, Sex and Reproduction

A new brand of “scientific” dating has sprouted up. It draws on an idea wrote about in the Chemistry of Kissing – basically, you have more snap, crackle and pop with someone who has an immune system very different to your own. Through your genes combined, the resulting offspring will have a stronger, more diverse immune system giving them an evolutionary advantage. Now this idea has been monetized to bring you GenePartner DNA Matching, because love is no coincidence.

For $99 US you get a kit so you can take a saliva sample and send it back to them for analysis. Two weeks later you’ll have your results, they’ll build up a profile for you, and you can start finding your perfect genetic match! *love*

What a service they offer too! They match partners based not only on how attracted you will be to them, but also how attracted they’ll be to you.

Plus they give you the probability of a successful pregnancy – which just feels like jumping the gun a bit to me. Really, you haven’t even MET the person and you want to know how likely it is you’ll get pregnant. I understand it’s super-important to some people, but it’s a bit ridiculous to expect a test like this to tell you about such a complicated thing as fertility.

The other bonus they list is that their site will prevent inbreeding. Then again I think the chances of accidentally inbreeding are pretty small. The world’s a big place, and most people know to look for a partner outside of their living room.

Honestly, DNA Dating, what will they think of next? Is there anything else they can cram science into in order to sell love?

Actually it reminds me of Gattaca, where they have booths set up where you can analyse stolen DNA from your lips after a kiss, or from the hair sample you swiped, if you’re that way inclined.

Arr!!! I think there be nothing wrong with the old fashioned method of kissing people, it’s cheaper! Who’s with me?

HeLa, the first immortal human cells and a tale of immorality

// January 12th, 2010 // No Comments » // Science Communication, Unethics

When we work with cell lines in the lab, we often work with HeLa cells. They can live in a vial of nutrients, and from a small sample you can grow a large quantity to use in cancer research, in vitro fertilisation research, stem cell research, virus research, pretty much any kind of human biology research actually. They’re a biologist’s wet dream.

HeLa cells come from an aggressive cervical cancer that attacked, and eventually killed, a women called Henrietta Lacks.

She has been dead for over 60 years but those cancer cells are still going strong. Which is pretty amazing! Usually when you take some cells out of a person they die pretty soon after, or they might live for a few months, but not 60 years. That’s rare. Cancer emerges after a lot of severe mutations and a Darwinian baptism by fire, only strong, successful mutants emerge from the ashes of their brothers who died from lethal mutations. The survivors are bad-ass.

They are also very weird looking. HeLa DNA has been extremely mutated, instead of 46 chromosomes it has 82, and it has several versions of human papilloma virus (HPV) DNA, which is found in pretty much every case of cervical cancer. So research with HeLa cells is NOT research with a normal human cell.

That strange DNA makes it do some pretty amazing things: It replicates abnormally fast, even for cancer cells, and it has an active copy of telomerase which means it can replicate indefinitely. Most other cells age as they divide until they reach the Hayflick Limit, then they don’t divide no more. Not HeLa. Neither do stem cells actually, but that’s a tale for another day.

HeLa cells revolutionised our understanding of human biology, but the family of Henrietta have yet to see a cent of it. In fact, those cells were taken from her without her knowledge. Dodgy, dodgy stuff. I’m placing this story firmly in the unethics basket just for that. HT to Ed Yong for telling us about a book soon to be released about the lady herself.

“The Immortal Life of Henrietta Lacks” comes out next month, written about the woman and the cells which should have made her famous. Rebecca Skloot been researching it for something like 10 years and it’s got some great reviews. I’m going to pre-order a copy, and if you’d like to know more about HeLa cells and Henrietta Lacks, do the same! It’s a story that deserves to be heard, and if there are enough pre-orders, Amazon will help promote the book. Plus it’s 30% off at the moment. What more could you want? Here’s the blurb.

Her name was Henrietta Lacks, but scientists know her as HeLa. She was a poor Southern tobacco farmer who worked the same land as her slave ancestors, yet her cells—taken without her knowledge—became one of the most important tools in medicine. The first “immortal” human cells grown in culture, they are still alive today, though she has been dead for more than sixty years. If you could pile all HeLa cells ever grown onto a scale, they’d weigh more than 50 million metric tons—as much as a hundred Empire State Buildings. HeLa cells were vital for developing the polio vaccine; uncovered secrets of cancer, viruses, and the atom bomb’s effects; helped lead to important advances like in vitro fertilization, cloning, and gene mapping; and have been bought and sold by the billions.

Intimate in feeling, astonishing in scope, and impossible to put down, The Immortal Life of Henrietta Lacks captures the beauty and drama of scientific discovery, as well as its human consequences.

Cheap date, grim reaper and swiss cheese – the world’s coolest gene names

// December 3rd, 2009 // 2 Comments » // Jibber Jabber, Just for Fun, Sex and Reproduction

I studied biochemistry at University, and I remember spending hours copying pathways, reading and rereading textbooks, then summarising, checking, drawing, testing, making mnemonics, in short EVERYTHING I could do to help me memorise things. There is a lot to remember in biochemistry, and a lot of words which don’t mean much that have to go in the right place. JAK activates JEK activates MEK which activates an enzyme which travels to the nucleus and binds to blah which attaches to blah region of the DNA and has the effect of increasing glucose absorption. Or something. Frankly I can’t remember anymore, and I’m damn glad I don’t have to try.

Meaningless acronyms are an annoying part of science, and of any job really. At work I talk about getting a tvc cadded, matching the key to the clapper and ingesting it – to anyone who hasn’t done TV advertising this is complete jibberish. Biochemistry is really no different – if you don’t know much about it, it’s because no one has explained it to you properly using normal words.

This post is not about normal words. Screw normal words! This is about the awesome, the spectacular, the creative and the downright weird.

These are some of the coolest names I have come across for proteins and genes, and a lot of them are found in the fruit fly Drosophila. Drosophila is the white lab rat of developmental science, it’s always the guinea pig because it reproduces REALLY fast, and creates multiple offspring in a single frenzy. Some other species (including humans) also get a mention in this list.

Tinman – Drosophila with a mutation to tinman develop with no heart.
Maggie – a mutation causes arrested development, in the Simpsons Maggie never ages.
Cheap Date – mutation causes Drosophila to be extra sensitive to alcohol. Another gene called Lush does the same thing.
Cleopatra – Cleopatra was killed by an asp, and interaction of mutant Cleopatra protein with the Asp protein is lethal.
Ken and Barbie – mutants (both male and female) lack external genitals.
Swiss Cheese – mutants have holes in their brain.
Grim Reaper – two separate genes, together they cause cell death.

For those biblically minded of us, there is Lot – mutants have more salt than usual, or Sarah – mutants are almost sterile, or Methuselah – mutants live extra long. Prefer Greek Myths? How about Ariadne, who showed Theseus how to get through the Minotaurs Labyrinth – in Drosophila, Ariadne mutants stop the axons of nerve cells finding their targets. Love Shakespeare (who doesn’t?), take Hamlet – which affects development of cells descended from IIB cells – “to be or not to be.”

Sometimes the names help us remember how things link together, take these names from Arabidopsis thaliana, a small flowering plant that’s like the Drosophila of plant genetics. Superman mutants have extra stamens in their flowers, while the Clark Kent is a milder version of the mutation, and Kryptonite suppresses the function of Superman.

Zebrafish have some neat ones too – including one-eyed pinhead, cyclops and squint – all important in the development of an embryo.

How about in humans? Well yesterday I talked about a spiky little protein called Sonic Hedgehog, which was originally found in, you guessed it, Drosophila, but which plays an important role in embryo development in humans. There’s not a huge number of genes with cool names in humans, and there’s a good reason for that. Imagine you had a child who was very sick and you met with the doctor, who looked at you seriously and said “I’m sorry, it’s genetic. Your son has a mutation in the Sonic Hedgehog gene.” There are a couple of others, like Tigger which is a segment of DNA which hops around into different locations

Those are my faves, but there’s plenty more out there. These are samples from My Favourite Gene Names and Gene Names by Organism, and I know there’s others that didn’t make the list. FlyNome has a searchable database of heaps of Drosophila genes and the story behind them. It’s almost worth getting into Drosophila research just for the cool names, plus imagine if you found a new gene and got to name it yourself… oh the possibilities…

Too Many Chromosomes!

// September 16th, 2009 // 2 Comments » // How Things Work, Sex and Reproduction

Todays installment of Reproduction Wednesday is about having too many chromosomes. The scientific term for this is aneuploidy, and the pirate term for this is “thar be too many etchings on yer peg leg!” Peg leg being a euphemism, in this case, for genetic material.

For the scientists among us – aneuploidy usually arises from failure of all the chromosomes to adhere to the mitotic spindle, causing one daughter cell to lose one copy of a chromosome, and the other to gain an extra copy of a chromosome.

For the non scientists – before yer cells split to form two new cells, they double their DNA and keep each chromosome joined together in the middle so as to keep ‘em together. Then all the chromosomes line up in the middle of the cell, and a rope from each end of the cell (for lack of a better nautical term) attaches to each chromosome, so as to break them apart from where they are joined. If this messes up and they miss a chromosome duplicate, then one cell will end up with too many chromosomes and one too few. When it happens correctly, it looks like this in pictorial form!

This can happen either in the egg or the sperm, or in the embryo when it is only a few cells old. When it does happen it is generally VERY BAD. There are a lot of checks that an embryo has to pass before it can be brought to term, and generally having too many chromosomes means a fail, and it will not implant or it will miscarry early in the pregnancy.

There are a couple of exceptions to the you-fail-you-die-now dogma, the most common of which is Down’s Syndrome. People with Down’s Syndrome have three copies of chromosome 21 (5% of the time they have two copies of chromosome 21 and a little bit extra chromosome 21 attached to another chromosome. Isn’t genetics weird!) Most of the time it is the egg that screwed up and provided the wrong number of chromosomes. Interestingly (or perhaps, terrifyingly depending on your outlook) the chances of having a baby with Down’s Syndrome increases with the age of the mother, at age 20 it is 1 in 1500, but at age 40 it is more like 1 in 60. Ouch.

Other syndromes that arise from this kind of genetic miscalculation include Edwards Syndrome (three copies of number 18) and Patau Syndrome (three copies of number 13). These embryo’s rarely come to term, and only 10% of those that do survive past the first year.

Aneuploidy is not as bad when it concerns the sex chromosomes, good old X and Y. Having three copies of X doesn’t seem to make any difference to a woman. This could be because only one X is active in a female, the other one (or two, if you’ve got it) is wound up tightly in an inactive form called, piratey enough, a Barr Body. Similarly a boy with two Y’s an X is generally just the same as normal. XXY is not so great for a guy, as they usually end up sterile.

This stuff (aneuploidy I mean) happens in cancer too, an excessive amount! But that is a story for another time… Now I must away to see Up at the movies with Sexy Man!

Further info on aneuploidy can be found at this site, I heartily recommend it!

Sickle Cell Anemia and Genetic Fence-Sitting

// June 22nd, 2009 // 5 Comments » // How Things Work

Following on from the theme of biological errors and the noise of life, I thought I’d talk about sickle cell anemia, quite a common ailment inherited Mendelian fashion through recessive genes.

If you’re new (very new) to genetics, then check out a picture for what I mean by recessive, and click through to Wikipedia to explain it all (man I love Wikipedia, is it natural to love an online encyclopedia of dubious accuracy? It feels so RIGHT!) Anyways, in the picture white is the recessive gene, and the flower will only have a white phenotype (as in, looks white) if both versions of the genes are the white recessive one.

Substitute red with normal haemoglobin (Hb), and white with mutated haemoglobin (HbS – S for Sickle or Screwed) and that’s what’s going on with sickle cell. If both your copies of haemoglobin have the sickle cell mutation, then you get the door prize – haemoglobin that tends to polymerise when it releases oxygen to form long rods (hehe, long rods) in the red blood cells, making them look all deformed and shabby like thus:

Shaped like a moon, or a sickle – think Grim Reaper!

Okay, I’m being a bit jokey about this, but it’s actually an awful disease – the cells are the wrong shape, and get caught in the blood stream causing blockages, which means progressive organ damage and pain, and they also don’t last as long (10-20 days rather than 120 days) causing anemia. Most people die early.

The weird thing is – this is terrible disease has been around for a long time with a clear genetic link – why hasn’t Darwin fished out out the mutation from the gene pool yet?

Researchers think that the sickle cell mutation was actually selected FOR, because there is evidence that having one copy of HbS and one normal Hb gene protects people against malaria.

Malaria is a highly lethal disease caused by protozoa carried by mosquitos, and even today kills about one million people a year. People who have African heritage often have a higher incidence of sickle cell, because malaria is endemic there. So the picture looks more like this -

You’re damned if you do and damned if you don’t, but all good if you’re a genetic fence-sitter and take one of each. Indecision for the win!

(Wish I could take credit for the pictures, but still setting up the computer… it arrived yesterday – yay! It’s very sexy)