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Citizen science class: Using the “bigfoot genome” for 21st century biology aimee whitcroft Mar 26

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Those of you who read this blog regularly (or not) will likely have picked up that I have something of a passion for things involving citizen science and education-type stuff. So, with that in mind, I present to you ‘science: cryptogenomics – using the “bigfoot genome” for 21st century biology‘.

cryptogenomics_-___the__bigfoot_genome_

The class is being run through Chalkle, a local and award-winning education platform/community. What’s it all about, though, and what will you get out of it? According to its description:

Earlier this year researchers claimed to have published a bigfoot genome sequence.

We will use publicly available tools and data to learn what they actually sequenced, then compare their results to those of recent studies that really used DNA evidence to show the existence on different human species.

what you will learn

Learn how to use free on-line tools to compare the genetics of the “sasquatch sequence” with other known species – all from your own laptop!

You’ll come away knowing:

  • what the tools are
  • where to access them,
  • how they work and
  • finally be able to figure out where ‘sasquatch’ is descended from and whether it’s real or not!

 

It’ll take place on April 2, 2013, in the evening, in Wellington CBD. Cost is a piffling $15 a person, you don’t need to have any prior expertise (yay!) and there are tonnes more details and instructions on signing up on the class’s page.

Oh, and did I mention the class is being run by fellow Sciblogger, ‘epic science communicator’, evolutionary geneticist extraordinnaire and all-around lovely chap Dr David Winter?

So, SO many reasons to go along. SO MANY*.

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* One of which, if I have facts straight, is that this is the first actual ‘citizen science’ class that Chalkle has run. So let’s show some support and have more things like this in future!

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Related posts:

Why aren’t more Kiwis involved in the International Space Apps Challenge?

Open course: Science from Superheroes to Global Warming

A bunch of others – just rummage through my blog :P

 

 

Tim Minchin explains ENCODE aimee whitcroft Sep 13

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Well, here’s a fun little treat for your 10:30 teatime today.

Anybody following the science news in the last week or two will have heard of the ENCODE results. Basically, we’re just taken a big step towards understanding the complexity of the human genome, and how it all works.  Which is good for a bunch of things, including disease treatment.

What is this big step?  Well, thanks to ENCODE, we now have a much better idea of how our genes are _controlled_ (or regulated, if you want to use the proper term).  It’s all quite complicated, but very interesting.

And now, brilliant comedian Tim Minchin* has produced a video, with nature, called ‘The Story of You: ENCODE and the human genome ‘. Watch and enjoy :)

Related posts:

Peter Dearden explains the ENCODE results over on Southern Genes.

You can also download your copy of the ENCODE poster over on Grant Jacobs’ blog Code for Life.

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* If you don’t know who he is, you should. I guess the first place to start would be to watch Storm, but he’s done a bunch of other, brilliant stuff too. Huzzah mad gingers!

Introducing a new blog: Southern Science aimee whitcroft Aug 31

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Hurrah!

go banner 3.1

Today, I introduce the first of a number of new bloggers starting over the next few months.  The Southern Genes blog, to be contributed to by a number of people from Genetics Otago, aims not only to talk about genetic science, but also to examine its effects on our society and to showcase some of the brilliant work which goes into it.

Welcome, everyone, and we look forward to all that lovely knowledge you’ll be sharing :)

Why the Caster Semenya sillyness makes me so angry aimee whitcroft Aug 24

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I am, I would be the first to admit, generally pretty flippant and light-hearted in my blogging.

semenya

Caster Semenya. I dunno, but Jenny Meadows looks at least as...hardcore...ya?

Not for me the heavy-handed nor overly serious style adopted by many others.  No, I prefer that my readers have a bit of a giggle, maybe pick up some new knowledge, and go skipping off into the rest of their day.

Not today, gentle readers, not today.

Upon perusing our fine print news media this morning (in this case, the NZ Herald), I was at first nonplussed, and then furious, to see yet another article about Caster Semenya.  The female athlete who won the 800m and 1500m races in the World Championships last year and then proceeded to be paraded (unkindly, often) in front of the world, by the media.

What occasioned this treatment?  Well, she won.  By quite a margin.  Performances like hers, in any sport, do tend to raise the eyebrows of sporting officials, as they suspect foul play of some sort.  Her 800m time beat her personal best (9 months earlier) by 7 seconds, and became a national, championship and world record time.  Now, I believe that a drug test in this case is perfectly fair.  They also, however, asked her to undergo a gender test.  This was supposed to be kept confidential (gender is, after all, somewhat more personal than drug use*), but was leaked to the press.

Who proceeded to have an absolute field day with the issue but, as is so often the case, I haven’t actually heard much sense from people around me who I’ve heard discussing it (although there were a couple of decent articles at the time).  The issue died down for a while, but has raised its ugly head again, and I am once again spittingly angry at the pronouncements by so many, who know so little, on the subject.

Before I get into said debate, some facts to bear in mind.

Gender is not, as many might believe, a binary characteristic.  In fact, like so much of life, genetics and the human experience, it encases a spectrum of different possibilities.  Some examples below:

- Superfemales/supermales – These are people who have an extra sex (X/Y) chromosome.  In females, for example, it means the that the person has 3 X chromosomes**, and some women can be taller (although other potential characteristics include reduced muscle tone and clumsiness).

- Congenital adrenal hyperplasia – Occurring in 1 in 1,000 people, this refers to a series of diseases in which the genes for enzymes which are involved in making cortisol have mutated.  The outcome?  Most of the time, it changes how much sex steroids people make (either too much or too little), which can affect their development, fertility, etc

- Conditions such as AID – Androgen insensitivity syndrome is caused by mutations in the androgen (male sex hormone) receptors.  People with the condition, which also, as with most genetic disorders, varies in strength and effect, often experience some level of infertility/undervirilisation.  In people who have complete AIS, a genetically male person (XY) will present externally as a female, as androgens are responsible during development for the development of a neutral foetus into a male foetus (one might describe being female as largely default).

And the tests for gender are far from, well, seriously accurate in some cases. To explain – gender is determined by whole chromosomes full of genes.  So to figure out whether someone is genetically male of female, you’re looking for very specific bits.  Which, even if a full sequence is done, is apparently something like a fishing expedition.  Other ways to test include looking at genes elsewhere, which regulate hormone production and sit elsewhere in the genome.  But again – not exactly back and white.  Or you could look at muscle, but the same applies***!

I’m certainly not going to try and guess what, if anything, might be affecting Caster Semenya – I’m simply trying to make clear that human gender is a far, far more complicated thing than simply being a boy or a girl.

And here’s where we can start the debate.  There are certainly a number of facets, so I’m going to try not to waffle, but rather open them up for discussion.

Privacy

Is this something something that should be being splayed across the media internationally?  Yes, something interesting is occurring.  And it’s not like doping, because that’s breaking the rules. Caster has broken none so far, and should be treated with a little bit of common decency (clearly, dignity is too much to ask). A lot of the complaining really does seem to have a very base, greenish tint to it…

And I thought we’d got over wanting to peer at other people in some sort of weird carnival-type fashion (especially if they didn’t consent).

Where do we draw the line?

This is the crux of it, I think.  It could be argued that most professional athletes are far from representative of the norm – like many models, they represent the far ends of the bell curve which makes up humanity.  Female athletes, for example, are likely to have started out with more androgens (male sex hormones) that their ‘normal’ counterparts, which would provide an advantage.  And we don’t moan about that.

Or, perhaps, one female athlete is taller than another – perhaps even taller than some male athletes.  Do we then tell her to compete with men? Obviously, asking shorter men to compete against women would probably still be unfair…

To give another example: Usain Bolt.  The man who made the world’s draw drop with his incredible speed, charm, and, well, that wonderful moment when he slowed down at the end of the race to show off a little.  He’s a complete freak .  Speed is made up of a mixture of how long your stride is, and how fast you can move your legs.  Bolt’s stride is unusually long (7ft or something equally incredible), and he is able to move those legs of his very fast, both of which give him that gobsmacking ability to outrun lightning.  Now, should we be saying that he can’t compete at all, since he’s basically untouchable (and going to get faster)?  I have heard not even the slightest whisper of such a suggestion.

Or, should we split athletes in classes, either instead of/in addition to splitting them by gender?

I dunno, perhaps we should do away with professional athletes completely, and just pull random people off the streets to compete.  Hmmph.

Other angles

Here’s where I bring in transhumanism, and prosthetics, and so forth.

A word on prosthetics.  Take, if you will, the case of Aimee Mullins****.  She’s a runner, and a gifted one at that.  She’s also a model, an inspirational speaker, and, oh yes, she wears prosthetic legs. And there’s Oscar Pistorius, who runs so fast on his prosthetic legs that he’s able to compete (and compete well) against able-bodied runners.

Which brings up another question: are prosthetics an unfair advantage? Should we ban their use, or have runners using them run in yet another category? Might athletes one day choose to lose limbs in favour of bionic alternatives?

That last point dips deeply into transhumanism, a subject with which I’m fascinated.  (For myself, I’d be happy to swap squishies for more advanced versions with cool features, but yes).

In conclusion

Certainly I don’t have answers, but I think we need to be very careful in the proscriptions we make – there’s much of the slippery slope about this whole issue.

And there’s no one test which will answer this question – it’s something for the judges to decide, as they figure out what constitutes female vs male. This is a matter for experts, not the the ill-informed opinions media/public debate.

Certainly, it would be nice if everyone could have a little more dignity as the decisions are made – at least as much dignity as Semenya has displayed during this time.

UPDATE: The IAAF has come to a decision on this.  Which makes the continuing media farce even more appalling.

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Postscript: Let me be clear – I understand why sporting events are split into male/female, and I have no problem with it.  Oh yeah, and also: the athlete who was moaning that running against Semenya was like running against a man, finished 8th. It could be argued that it’s not Semenya getting in her way…and there’s nothing uglier than bad sportsmanship.

Further postscript: Jenny Meadows actually came out in support of Semenya last year – details of decent sportsmanship in this article.

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* Particularly, and I should stress this, in countries which are not western and liberal!  Good grief, South Africa (from whence I hail) has some seriously old-school attitudes towards such things, and the poor girl’s only 19 now!

** Other names for the condition include triplo-X, trisomy X, XXX syndrome, and 47,XXX aneuploidy

*** Basically, while men and women differ in muscle strength and muscle variation, there are always going to be outliers on both sides.

**** Watch TED talks by her, here.

Sperm of a feather clump together aimee whitcroft Jan 22

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I’m gobsmacked.  And highly amused, as well (it’s the immature part of me, apologies).

deer mouseCredit: Phil Myers (photographer, copyright holder), Museum of Zoology, University of Michigan.  More info here and here.  (I tried to find a picture of sperm in question, but nothing seemed to be (c)-free)

Research published in Nature this week has shown something incredible – sperm may not be the mindless automatons bethought by many of us.

Instead, researchers have found that the sperm of deer mice (which are notoriously slutty) are actually able to differentiate between their siblings (i.e. spermies from the same male) and the sperm from competing, and hence arch-rival males.

And how do these family-focussed sperm then deal with the situation?  Not with insults, no, nor the smashing of the headlights of each others’ cars. After identifying the sperm most genetically related to them, they then clump together, allowing them to swim faster towards the egg than less cooperative/clumped together sperm.  Fascinatingly, it’s not a binary relationship – i.e. sperm from same male vs all other sperm.  Sperm were more likely to, for example, aggregate with sperm from their male’s'sibling than with those from an unrelated male.

The behaviour has clear links to the promiscuity of the species – sperm in the Oldfield mouse (a related monogamous species) aggregated without any preference for relatedness.  So why the difference?  Well, one hypothesis posits that aggregation allows the sperm to swim faster, or navigate obstacles better (the mind boggles) – in largely monogamous species which sperm hang out with which clearly isn’t an issue.  As one might expect, however, in species where the sperm of multiple males is vying for the same egg, it would be far better to give a hand up to sperm which are related to one, as opposed to helping out one’s opponents.

Another hypothesis is that the Peromyscus genus was originally promiscuous and that sperm aggregation arose before the two species (deer and Oldfield mouse) diverged, but the ability to discriminate only developed afterwards.

And it would seem to be a clear function of adaptation through sperm competition.

The mechanism which allows this clumping is simple – whereas human sperm have rounded heads, these sperm actually have hook-shaped heads.

Of course, the scientists are completely mystified as to how the sperm are able to make both the differentiation and follow-up action, but no doubt they are eagerly striving to understand these things (I know I would be).  The closest they’ve got thus far is to suggest that it may be a simple genetic mechanism of some kind (as in the case of similarly selective cooperations seen in some social amoeba).

And: I included the picture below, again of a deer mouse, because I think it’s an hilariously fantastic example of the evil eye…

deer mouse 2Credit: Phil Myers (photographer, copyright holder), Museum of Zoology, University of Michigan.  More info here and here.  (I tried to find a picture of sperm in question, but nothing seemed to be (c)-free)

Reference:
Fisher, H., & Hoekstra, H. (2010). Competition drives cooperation among closely related sperm of deer mice Nature DOI: 10.1038/nature08736


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