Saturday, 5 July 2014

STAP retractions are both a failing and a triumph of science

It was looking inevitable and this week two high profile Nature articles on “STAP” (stimulus-triggered acquisition of pluripotency) stem cells were finally retracted in Nature:

Several critical errors have been found in our Article and Letter (http://dx.doi.org/10.1038/nature12969), which led to an in-depth investigation by the RIKEN Institute. The RIKEN investigation committee has categorized some of the errors as misconduct (see Supplementary Data 1 and Supplementary Data 2). Additional errors identified by the authors that are not discussed in RIKEN’s report are listed below.

...

We apologize for the mistakes included in the Article and Letter. These multiple errors impair the credibility of the study as a whole and we are unable to say without doubt whether the STAP-SC phenomenon is real. Ongoing studies are investigating this phenomenon afresh, but given the extensive nature of the errors currently found, we consider it appropriate to retract both papers.

Nature cover the retractions in an editorial, “STAP retracted”, which runs with the tagline,

“Two retractions highlight long-standing issues of trust and sloppiness that must be addressed.”

You can get a sense of those issues from the retraction statement and the editorial, which concludes:

“we and the referees could not have detected the problems that fatally undermined the papers. The referees’ rigorous reports quite rightly took on trust what was presented in the papers.”

They also highlight “sloppiness” in science, manifest as a “growth in the number of corrections reported in journals in recent years”. (Something not helped, in my opinion, by high profile journals such as Science and Nature burying so much of the important methods in Supplementary Data, which is rarely reviewed or edited as critically as material in the main text body.)

You can read more about those issues in the editorial and elsewhere, such as the Faculty of 1000 blog. The STAP papers, their initial irreproducibility and eventual retraction highlight potential failings of the current scientific system, which places far too much emphasis on output quantity and impact rather than (true) quality and integrity.

However, they also highlight the tremendous success of the scientific system.

The fact is, the experiments were repeated, the failure to reproduce results was documented, suspicions were raised and investigations made. Science works because, ultimately, you cannot fake it. Whatever data you make up, whatever results you misinterpret, whatever sloppiness leads to “conclusions [that] seem misleadingly robust”, the truth will out eventually. You cannot hoodwink nature.

And that is why science remains far and away the best (probably only) method we have for establishing the truth about reality. The system maybe flawed, it may waste money and it may lead poor unsuspecting suckers chasing wild geese, but eventually it will self-correct. So, whilst I would never put my trust in individual scientists (unless they have earnt it) or results, and I remain skeptical of every new claim, I still emphatically trust science itself.

Saturday, 28 June 2014

A comprehensive overview of chemical-free consumer products

If, like me, you get a bit annoyed by people who decry “chemicals” (and are usually far too trusting of anything “natural” at the same time), you will appreciate an online paper just published at the Nature Chemical Biology blog, “A comprehensive overview of chemical-free consumer products” by Alexander Goldberg and CJ Chemjobber.

I think that the message is so important, I have reproduced the entire abstract main text of the paper:

Manufacturers of consumer products, in particular edibles and cosmetics, have broadly employed the term ‘Chemical free’ in marketing campaigns and on product labels. Such characterization is often incorrectly used to imply — and interpreted to mean — that the product in question is healthy, derived from natural sources, or otherwise free from synthetic components. We have examined and subjected to rudimentary analysis an exhaustive number of such products, including but not limited to lotions and cosmetics, herbal supplements, household cleaners, food items, and beverages. Herein are described all those consumer products, to our knowledge, that are appropriately labelled as ‘Chemical free’.

Exactly.

Friday, 27 June 2014

Don't put plastic bags in recycling bins

Without recycling - especially plastic recycling - we're all doomed. Seriously. But what’s possibly even more tragic than selfish people who don’t bother to recycle when the service is offered, is people who go to the effort of sorting their recycling and then completely nullify their effort by sticking it in a plastic bag.

There’s some good information on why this is so bad at Planet Ark. It’s worth repeating the main points here:

Human health and our natural resources

The first level of sorting at recycling stations is done by hand.

Workers at the recycling station are sorting through tonnes of material an hour and don’t have time to open bags to find out what’s inside. Your plastic bags could be filled with recyclable material like glass or plastic bottles or aluminium cans. Or they could be full of contaminants like food scraps, plastic wrap or unwanted wine glasses. Even worse, they could be full of dirty or dangerous material like dirty nappies or medical equipment.

Since it’s too dangerous and time consuming to open and sort the bags, they have to be removed from the recycling stream and thrown into the rubbish. That means valuable resources will not be reclaimed. Instead they will be wasted in landfill.

Recycling system efficiency

The next issue with plastic bags is that they interfere with the automatic sorting machines.

Conveyor belts feed the recycling into rotating tunnels, onto spinning wheels and past magnets and eddy currents to separate the plastic, glass, paper, aluminium and steel cans. Plastic bags cannot be sorted from other materials by existing machinery. Instead, they get caught in the conveyor belts and jam spinning wheels and can bring the entire sorting station to a halt. The bags then need to be found and removed by hand - a time consuming and often dangerous process that reduces the overall efficiency of the recycling station or materials recovery facility (MRF).

The photo above shows the sign on all of the recycling bins in our building. Despite this, people still keep putting plastic bags in recycling bins! When I dropped down some recycling earlier this week this is what I found:

Being a good citizen (and without any other crap in the bin), I emptied it out and stuck the bag in the regular bin. Usually, I am not so brave.

It left me feeling angry at the laziness and/or ignorance that made someone think that this was acceptable behaviour. If you see someone put plastic bags in recycling, please tell them not to. And if you do… Stop! Put them in the regular bin or, better still, a dedicated plastic bag recycling bin at your local supermarket (if it has one).

Thursday, 26 June 2014

Earthworks 2013 Barossa Valley Shiraz

From (mostly) Aussie beer to Aussie wine. This week's discovery was Earthworks 2013 Barossa Valley Shiraz. It’s a real corker. Except no cork, obviously. (The Aussies were sensible enough to ditch those years ago.)

A good companion for beef and guinness stew. And blogging! The only downside is a very purple tongue.

The best bit… I bought it on buy-one-get-one-free, so we still have another bottle to enjoy!

Wednesday, 25 June 2014

The tragic wonder of life on Earth today

A sad post over at Why Evolution Is True today: “Last chance to see… pretty much everything, including these Dolichopodids”, reporting on the gloomy effects of systemic neonicotinoid insecticide use... plus some pretty insect pictures.

We are lucky to be alive today. It is probably the only moment in Earth’s history and future in which the technology exists to capture images and videos of creatures great and small, whilst those creatures still exist to marvel at.

It is sad to think that the next generation will not be so fortunate. It’s time that politicians paid more attention to scientists and environmentalists, for the sake of everyone and everything.

Tuesday, 24 June 2014

A pale ale beer tasting

The Saturday before last, we were with friends watching England experience their first (but least upsetting) sporting defeat of the past couple of weeks: a tight one point Rugby Union loss to the All Blacks. Despite the defeat, it was a good game and made all the more enjoyable by a fine array of beverages.

In fact, the disappointment of the rugby was over-shadowed by the impromptu pale ale beer tasting that accompanied it. The line up is above, and started with Haymaker, an English import from Hook Norton in the Cotswolds. It was quite strong for a pale ale, at 5% alcohol, but packed full of flavour. Yum.

After that it was on to the Aussie beers. We’d brought some Beechworth pale ale from Bridge Road Brewery, which was good and fruity with a quite hoppy taste. Another craft brewery to add to my increasing watchlist and another fine pale ale to add to the existing favourites. One fifty lashes from James Squire is already on that list, being one of the first decent* beers that I discovered in Australia. (*To my taste.)

Only the final beer let the side down: Coopers was by far and away the worst and, after the others, I have nothing good to say about it. If only it could have been replaced with Fat Yak from Matilda Bay, it would have been a first class collection!

Monday, 23 June 2014

XKCD hits the spot again on climate change

A couple of weeks old but no less poignant:

Climate change deniers are quick to point out that there was still life on Earth at predicted future CO2 levels and global temperatures. This is true. The problem is, that life did not include us, anything like us, or even anything much like most of the things we eat. Oh yes, and most of the world’s major cities being under water. :sigh:

It’s a position summed up frustratingly well by Doonesbury (via WEIT):