Science Bloggers vs. Science

First NASA had quite possibly discovered an alien lifeform.

Then it was an earth bacteria that has a unique kind of arsenic-based DNA - an entirely new kind of organism.

Then it merely could use arsenic in its DNA, if forced to, although under normal conditions it didn't.

But now, it's looking like it's just a regular (albeit tough) bug - and a lot of hot air.

*

The "arsenic-based alien bacteria" story attracted more media attention than any other scientific paper of the last year. At first, I was very pleased by this: to a scientist, the discovery of an organism that can use arsenic instead of phosphorous in its DNA would have been massive news, with big implications for every branch of biology. How great that the media picked up on the importance of this story, even though it's about a specialized point of biochemistry, I thought.

Unfortunately, as you've probably heard, serious questions have been asked about the Science paper announcing the findings. For details, see microbiologist Rosie Redfield's devastating post on the topic: Arsenic-associated bacteria (NASA's claims), and this one from Alex Bradley: Arsenate-based DNA: a big idea with big holes. In a nutshell, the critics make a very strong case that the evidence supposedly showing arsenic-containing DNA is flawed, and fairly obviously so.

As I've said before, this kind of thing is why science blogging is so important. Thanks to bloggers such as those I've linked to, and many others, this paper - which has enormous implications, if true - has been subject to detailed scrutiny within days of publication.

Without blogs, these questions would certainly have been asked sooner or later - but with the emphasis on "later". The traditional way to criticize a paper is to write a Letter to the Editor of the journal that published it but this usually takes, at best, weeks, and usually months to appear.

Some journals now feature "e-letters" which can appear within hours, or public comment threads attached to each paper, and this is certainly a big step forward. Blogs still have the edge, though, because it's often hard to incorporate pictures, html, etc. into these comments, and these discussion threads often become very hard to read as the important comments get mixed up with less useful, or simply out of date, ones.

A blog post, clearly setting out the arguments, and updated as new information comes to light, is, to my mind, the best form of scientific peer review we currently have.

Science Bloggers vs. Science

First NASA had quite possibly discovered an alien lifeform.

Then it was an earth bacteria that has a unique kind of arsenic-based DNA - an entirely new kind of organism.

Then it merely could use arsenic in its DNA, if forced to, although under normal conditions it didn't.

But now, it's looking like it's just a regular (albeit tough) bug - and a lot of hot air.

*

The "arsenic-based alien bacteria" story attracted more media attention than any other scientific paper of the last year. At first, I was very pleased by this: to a scientist, the discovery of an organism that can use arsenic instead of phosphorous in its DNA would have been massive news, with big implications for every branch of biology. How great that the media picked up on the importance of this story, even though it's about a specialized point of biochemistry, I thought.

Unfortunately, as you've probably heard, serious questions have been asked about the Science paper announcing the findings. For details, see microbiologist Rosie Redfield's devastating post on the topic: Arsenic-associated bacteria (NASA's claims), and this one from Alex Bradley: Arsenate-based DNA: a big idea with big holes. In a nutshell, the critics make a very strong case that the evidence supposedly showing arsenic-containing DNA is flawed, and fairly obviously so.

As I've said before, this kind of thing is why science blogging is so important. Thanks to bloggers such as those I've linked to, and many others, this paper - which has enormous implications, if true - has been subject to detailed scrutiny within days of publication.

Without blogs, these questions would certainly have been asked sooner or later - but with the emphasis on "later". The traditional way to criticize a paper is to write a Letter to the Editor of the journal that published it but this usually takes, at best, weeks, and usually months to appear.

Some journals now feature "e-letters" which can appear within hours, or public comment threads attached to each paper, and this is certainly a big step forward. Blogs still have the edge, though, because it's often hard to incorporate pictures, html, etc. into these comments, and these discussion threads often become very hard to read as the important comments get mixed up with less useful, or simply out of date, ones.

A blog post, clearly setting out the arguments, and updated as new information comes to light, is, to my mind, the best form of scientific peer review we currently have.

Online Comments: It's Not You, It's Them

Last week I was at a discussion about New Media, and someone mentioned that they'd been put off from writing content online because of a comment on one of their articles accusing them of being "stupid".

I found this surprising - not the comment, but that anyone would take it so personally. It's the internet. You will get called names. Everyone does. It doesn't mean there's anything wrong with you.

I suspect this is a generational issue. People who 'grew up online' know, as Penny Arcade explained, that

The sad fact is that there are millions of people whose idea of fun is to find people they disagree with, and mock them. And they're right, it can be fun - why else do you think people like Jon Stewart are so popular? - but that's all it is, entertainment. If you're on the receiving end, don't take it seriously.

If you write something online, and a lot of people read it, you will get slammed. Someone, somewhere, will disagree with you and they'll tell you so, in no uncertain terms. This is true whatever you write about, but some topics are like a big red rag to the herds of bulls out there.

Just to name a few, if you say anything vaguely related to climate change, religion, health, the economy, feminism or race, you might as well be holding a placard with a big arrow pointing down at you and "Sling Mud Here" on it.

The point is - it's them, not you. They are not interested in you, they don't know you, it's not you. True, they might tailor their insults a bit; if you're a young woman you might be, say, a "stupid girl" where a man would merely get called an "idiot". But this doesn't mean that the attacks are a reflection on you in any way. You just happen to be the one in the line of fire.

What do you do about this? Nothing.

Trying to enter into a serious debate is pointless. Insulting them back can be fun, just remember that if you find it fun, you've become one of them: "he who stares too long into the abyss...", etc. Complaining to the moderators might help, but unless the site has a rock solid zero-tolerance-for-fuckwads policy, probably not. Where the blight has taken root, like Comment is Free, I'd not waste your time complaining. Just ignore it and carry on.

The most important thing is not to take it personally. Do not get offended. Do not care. Because no-one else cares. Especially the people who wrote the comments. They presumably care about whatever "issue" prompted their attack, but they don't care about you. If anything, you should be pleased, because on the internet, the only stuff that doesn't attract stupid comments is the stuff that no-one reads.

I've heard these attacks referred to as "policing" existing hierarchies or "silencing" certain types of people. This seems to me to be granting them far more respect than they deserve. With the actual police, if you break the rules, they will physically arrest you. They have power. Internet trolls don't: if they succeed in policing or silencing anybody, it's because their targets let them boss them around. They're nobody; they're not your problem.

If you can't help being offended by such comments, don't read them, but ideally you shouldn't need to resort to that. For one thing, it means you miss the sensible comments (and there's always a few). But fundamentally, you shouldn't need to do this, because you really shouldn't care what some anonymous joker from the depths of the internet thinks about you.

Online Comments: It's Not You, It's Them

Last week I was at a discussion about New Media, and someone mentioned that they'd been put off from writing content online because of a comment on one of their articles accusing them of being "stupid".

I found this surprising - not the comment, but that anyone would take it so personally. It's the internet. You will get called names. Everyone does. It doesn't mean there's anything wrong with you.

I suspect this is a generational issue. People who 'grew up online' know, as Penny Arcade explained, that

The sad fact is that there are millions of people whose idea of fun is to find people they disagree with, and mock them. And they're right, it can be fun - why else do you think people like Jon Stewart are so popular? - but that's all it is, entertainment. If you're on the receiving end, don't take it seriously.

If you write something online, and a lot of people read it, you will get slammed. Someone, somewhere, will disagree with you and they'll tell you so, in no uncertain terms. This is true whatever you write about, but some topics are like a big red rag to the herds of bulls out there.

Just to name a few, if you say anything vaguely related to climate change, religion, health, the economy, feminism or race, you might as well be holding a placard with a big arrow pointing down at you and "Sling Mud Here" on it.

The point is - it's them, not you. They are not interested in you, they don't know you, it's not you. True, they might tailor their insults a bit; if you're a young woman you might be, say, a "stupid girl" where a man would merely get called an "idiot". But this doesn't mean that the attacks are a reflection on you in any way. You just happen to be the one in the line of fire.

What do you do about this? Nothing.

Trying to enter into a serious debate is pointless. Insulting them back can be fun, just remember that if you find it fun, you've become one of them: "he who stares too long into the abyss...", etc. Complaining to the moderators might help, but unless the site has a rock solid zero-tolerance-for-fuckwads policy, probably not. Where the blight has taken root, like Comment is Free, I'd not waste your time complaining. Just ignore it and carry on.

The most important thing is not to take it personally. Do not get offended. Do not care. Because no-one else cares. Especially the people who wrote the comments. They presumably care about whatever "issue" prompted their attack, but they don't care about you. If anything, you should be pleased, because on the internet, the only stuff that doesn't attract stupid comments is the stuff that no-one reads.

I've heard these attacks referred to as "policing" existing hierarchies or "silencing" certain types of people. This seems to me to be granting them far more respect than they deserve. With the actual police, if you break the rules, they will physically arrest you. They have power. Internet trolls don't: if they succeed in policing or silencing anybody, it's because their targets let them boss them around. They're nobody; they're not your problem.

If you can't help being offended by such comments, don't read them, but ideally you shouldn't need to resort to that. For one thing, it means you miss the sensible comments (and there's always a few). But fundamentally, you shouldn't need to do this, because you really shouldn't care what some anonymous joker from the depths of the internet thinks about you.

My Christmas Wish List

Both my Dad and my Nono asked me what I wanted for Christmas. I'm not sure. I've been thinking about it for a while. But I'm really not sure.

There are somethings that I really like. But I don't know if they're too expensive to ask for. Or too late. But this is the list I came up with.

1. A Serger. My Nana has one. And I really like it. This is really all that I want. But I know that it's expensive.

2. A sewing box with sewing supplies.

3. Pretty fabric.

4. Some "I Love This Yarn."

5. A ring or headband from Much Love Illy.

6. Anything from Love Stitched.

7. Colorful tights.

8. A long coat like my Nana's. The one with the ruffles.

9. A wooden shoulder rest for my violin. :)

10. The movie Little Dorrit. I watched it with my Nana. And I really liked it.

11. More ribbon. I like making bows.

12. A pretty scarf with a fun pin.

That's my wish list. But I really just want a Serger. If I can't have that, I'd really like a wooden shoulder rest. I know that Christmas is more about giving that receiving. I'd rather be able to donate some money or toys to kids that wouldn't get anything. :)C

Autism and Old Fathers

A new study has provided the strongest evidence yet that the rate of autism in children rises with the father's age: Advancing paternal age and risk of autism. But questions remain.

The association between old fathers and autism has been known for many years, and the most popular explanation has been genetic: sperm from older men are more likely to have accumulated DNA damage, which might lead to autism.

As I've said before, this might explain some other puzzling things such as the fact that autism is more common in the wealthy; it might even explain any recent increases in the prevalence of autism, if people nowadays are waiting longer to have kids.

But there are other possibilities. It might be that the fathers of autistic people tend to have mild autistic symptoms themselves (which they do), and this makes them likely to delay having children, because they're socially anxious and so take longer to get married, or whatever. It's not implausible.

The new study aimed to control for this, by looking at parents who had two or more children, at least one of them with autism, and at least one without it. Even within such families, the autistic children tended to have older fathers when they were born - that is to say, they were born later. See the graphs below for details. This seems to rule out explanations based on the characteristics of the parents.

However, there's another objection, the "experienced parent" theory. Maybe if parents have already had one neurotypical child, they're better at spotting the symptoms of autism in subsequent children, by comparison with the first one.

The authors tried to account for this as well, by controlling for the birth-order ("parity") of the kids. They also controlled for the mother's age amongst several other factors such as year of birth and history of mental illness in the parents. The results were still highly significant: older fathers meant a higher risk of autism. As if that wasn't enough, they also did a meta-analysis of all the previous studies and confirmed the same thing.

So overall, this is a very strong study, but there's a catch. The study population included over a million children (1,075,588) born in Sweden between 1983 and 1992. Of these, there was a total of 883 diagnosed cases of autism. That's a rate of 0.08%. In other words, although older fathers raised the risk of autism by quite a lot relatively speaking, the absolute rate was still tiny.

The most recent estimates of autism prevalence in Britain have put the figure at somewhere in the region of between 1% and 2% e.g. Baird et al (2006) and Baron-Cohen et al (2009) with American studies, using slightly different methods, generally coming in just below 1%. So the Swedish figure is more than 10 times lower than modern estimates. Whether this reflects different criteria for diagnosis, national differences, or increased prevalence over time, is debatable but it does raise the question of whether these findings still apply today.

The only way to know for sure would be to do a randomized controlled trial - get half your volunteer men to wait 10 years before having children - but I don't think that's going to happen any time soon...

Hultman CM, Sandin S, Levine SZ, Lichtenstein P, & Reichenberg A (2010). Advancing paternal age and risk of autism: new evidence from a population-based study and a meta-analysis of epidemiological studies. Molecular psychiatry PMID: 21116277

Autism and Old Fathers

A new study has provided the strongest evidence yet that the rate of autism in children rises with the father's age: Advancing paternal age and risk of autism. But questions remain.

The association between old fathers and autism has been known for many years, and the most popular explanation has been genetic: sperm from older men are more likely to have accumulated DNA damage, which might lead to autism.

As I've said before, this might explain some other puzzling things such as the fact that autism is more common in the wealthy; it might even explain any recent increases in the prevalence of autism, if people nowadays are waiting longer to have kids.

But there are other possibilities. It might be that the fathers of autistic people tend to have mild autistic symptoms themselves (which they do), and this makes them likely to delay having children, because they're socially anxious and so take longer to get married, or whatever. It's not implausible.

The new study aimed to control for this, by looking at parents who had two or more children, at least one of them with autism, and at least one without it. Even within such families, the autistic children tended to have older fathers when they were born - that is to say, they were born later. See the graphs below for details. This seems to rule out explanations based on the characteristics of the parents.

However, there's another objection, the "experienced parent" theory. Maybe if parents have already had one neurotypical child, they're better at spotting the symptoms of autism in subsequent children, by comparison with the first one.

The authors tried to account for this as well, by controlling for the birth-order ("parity") of the kids. They also controlled for the mother's age amongst several other factors such as year of birth and history of mental illness in the parents. The results were still highly significant: older fathers meant a higher risk of autism. As if that wasn't enough, they also did a meta-analysis of all the previous studies and confirmed the same thing.

So overall, this is a very strong study, but there's a catch. The study population included over a million children (1,075,588) born in Sweden between 1983 and 1992. Of these, there was a total of 883 diagnosed cases of autism. That's a rate of 0.08%. In other words, although older fathers raised the risk of autism by quite a lot relatively speaking, the absolute rate was still tiny.

The most recent estimates of autism prevalence in Britain have put the figure at somewhere in the region of between 1% and 2% e.g. Baird et al (2006) and Baron-Cohen et al (2009) with American studies, using slightly different methods, generally coming in just below 1%. So the Swedish figure is more than 10 times lower than modern estimates. Whether this reflects different criteria for diagnosis, national differences, or increased prevalence over time, is debatable but it does raise the question of whether these findings still apply today.

The only way to know for sure would be to do a randomized controlled trial - get half your volunteer men to wait 10 years before having children - but I don't think that's going to happen any time soon...

Hultman CM, Sandin S, Levine SZ, Lichtenstein P, & Reichenberg A (2010). Advancing paternal age and risk of autism: new evidence from a population-based study and a meta-analysis of epidemiological studies. Molecular psychiatry PMID: 21116277