Posts filed under General (3156)

From Stuff:

Revolutionary new drugs that could cure terminal cancer should be on the market here within a few years but patients will have to be “super rich” to afford them.

One four-dose treatment of the drug now under clinical trials costs about $140,000 while other ongoing courses can cost hundreds of thousands of dollars

That’s one real possibility, but there are others.

Firstly, the new drugs might not be all that good. After all, we had some of the same enthusiasm about angiogenesis inhibitors in the late 1990s and about selective tyrosine kinase inhibitors a few years later. The new immunotherapies look wonderful, but so far only  for a minority of patients. And we’re seeing their best side now, from trials stopped early for efficacy.

Alternatively, they might be too effective.  The adaptive immune system is kept under the same sort of strict controls as nuclear weapons, and for much the same reason — its ability to turn the battlefield into a lifeless wasteland. The most successful new treatments remove one of the safety checkpoints, and it’s possible that researchers won’t be able to dramatically expand the range of patients treated without producing dangerous collateral damage.

Finally, there’s the happy possibility. If we get evidence that inhibiting PD-1 and other T-cell checkpoints is safe and broadly effective, everyone will want to make inhibitors, and we’ll get competition. Bristol-Myers-Squib has a monopoly on nivolumab, but it doesn’t have a monopoly on immune checkpoint inhibition. This is already happening, as Bruce Booth reports from the ASCO conference

Most major oncology players have abstracts involving PD-1, including Merck, BMS, AZ, Novartis, Roche, and pretty much everyone else.  Other T-cell related targets like CTLA-4, TIM-3, OX-40, and LAG-3 round out the list of frequent mentions

The drugs still won’t be cheap, because each company will need its own clinical trials, but the development risk will be much lower and the margin for rapacious price-gouging narrower, so they won’t be $140000 per patient for very long.

• Michael LaCour, the researcher accused of faking data in his study on changing opinions about same-sex marriage, has issued a response to the allegations today as he promised. Virginia Hughes at Buzzfeed and  Ivan Oransky at RetractionWatch have stories. I’ve seen a lot of comments about this on Twitter from people who work in empirical social sciences or in ethics. So far I haven’t seen anyone who is convinced by the response.

• There’s story in New York magazine about David Broockman, who found the problems, about the difficulty of reporting suspicions of fraud in research.  ““I think there’s an interesting metaphor between what I went through now and what I went through as a gay teenager,” Broockman says.

• The UK is introducing a ‘legal highs’ ban. The government are using a widely–quoted figure of 97 deaths in the last year due to legal highs.  As Vice.com explains, the figure is bogus in two ways. Firstly, the figure is based on detectable presence of a drug, not on it being even a contributing cause. Secondly and more importantly, the drugs in the majority of these cases were already illegal at the time.

• You’ve probably seen the Washington Post chart of deaths in World Cup construction. Unless you saw it at the original site, you may not have seen the disclaimer above it (emphasis added):

Some of these numbers (like Sochi’s) are third-party estimates, others (like Beijing’s) are based on official numbers that are almost certainly an undercount. And it’s tough to do an apples-to-apples comparison here, since the Qatar estimates include the deaths of all migrant workers after the announcement of Qatar’s successful bid in 2010, while other countries’ figures may only include deaths directly related to, say, stadium construction.

The exploitation of migrant workers isn’t new and it isn’t all Sepp Blatter’s fault. It’s one of the reasons Qatar was regarded as a terrible choice at the time.
Social media tends to spread images out of context, and this can be a problem if you’re trying to be seen as the sort of journalist who cares about facts.

• Far over the horizon in the opposite direction, there’s a former UK TV presenter ,now working in Qatar, who says there have been no construction-related deaths. And that there’s no problem with gay rights either.

Team Ratings for Round 12

The basic method is described on my Department home page.

Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 84 matches played, 47 of which were correctly predicted, a success rate of 56%.

Here are the predictions for last week’s games.

Predictions for Round 12

Here are the predictions for Round 12. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Team Ratings for Round 16

The basic method is described on my Department home page.

Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 99 matches played, 66 of which were correctly predicted, a success rate of 66.7%.

Here are the predictions for last week’s games.

Predictions for Round 16

Here are the predictions for Round 16. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Has the cure for cancer been with us all along? A vaccine in development. The details, tonight at seven. (Yes we are still here!)

— Campbell Live (@CampbellLiveNZ) May 25, 2015

The segment was about research from the Malaghan Institute, who are working on ways to encourage a patient’s immune system to attack tumours. They say, in a press release

While the research will focus specifically on targeting melanoma, it is anticipated that the methodology being developed could be applied to other cancers in the future.

The therapeutic vaccine approach differs from the preventative vaccines used to protect against diseases such as measles or the flu because the cancer vaccine is designed to be given to an individual after they have already shown signs of disease.

“It is known that white blood cells called T cells can kill tumour cells,” says Dr Hermans. “The cancer vaccines, which are custom-made for each cancer patient, are designed to stimulate the activity of these cancer-fighting immune cells.”

As the press release makes clear, the term ‘vaccine’ is technically correct, but liable to mislead: these are customised immune-system treatments specific to one tumour in one individual. It’s nothing like the measles vaccine that you get as an infant for lifetime protection.

Like other research groups, the Malaghan Institute are starting with melanoma. There are at least two reasons melanoma is a good place to start. The simple reason: until very recently, metastatic melanoma was completely untreatable, so anything would be an improvement. There’s also a complex reason: melanoma occasionally shrinks or vanishes of its own accord, apparently more often than other tumours do. The spontaneous regressions are presumably thanks to the immune system waking up and realising the tumour is a problem, so melanoma is a good starting point if you want to find out how this happens and encourage it to happen more often.

The basic problem is that the immune system tends to see cancer cells as part of the patient, since, fundamentally, they are. The Malaghan Institute has a innovative addition to the treatment, a chemical that scares specific parts of the immune system into action. They expect that combining this with the existing tumour vaccine approaches will give a more reliable result.

Malaghan got $4.5 million from the Health Research Council to work on this, which is pretty impressive given the HRC budget and competition, but the melanoma vaccine is still in the initial stages of testing. The majority of promising treatments going in to Phase I clinical trials don’t end up being useful. Even if this one does, that’s no guarantee it will work for other types of cancer, and while it’s a vaccine in the sense that it works by stimulating an immune reaction, it’s nothing like the vaccines we give to kids.

It’s not a good time to criticise Campbell Live, but although the Malaghan’s research is truly impressive, it’s not a general-purpose cure for cancer anytime this decade. And there’s a basic principle that you shouldn’t say “cure” in the headline unless there’s a cure.

• Stat of the weekend:  1,201,607 to 734,300.

• Flickr has an automatic photo-tagging algorithm. Users don’t like it, because tagging is their business. And also because it “labelled images of black people with tags such as “ape” and “animal” as well as tagging pictures of concentration camps with “sport” or “jungle gym.”

• “Analysis of samples from 55- to 73-year-olds found more than 100 DNA mutations linked to cancer in every 1 sq cm (0.1 sq in) of skin.“ That’s not telling us anything about risk, since we already know pretty accurately what the risk is. But if other cancers are at all similar, it’s a complication for drugs that target the cancer-causing mutations: the friendly-fire damage could be a real problem.

• A basic medical-reporting rule is that you don’t say “cure” in the headline if it isn’t a cure. The recent study of mutations in prostate cancer, reported in the Herald (from the Telegraph), is headlined “Breakthrough offers hope for prostate cancer cure“. About two-thirds of the tumours “had mutations in a molecule that interacts with the male hormone androgen which can already be targeted by current drugs.”  That’s true, but it’s not only “can already be targeted”, but also “is already targeted as standard practice“. Many of other commonly-found mutations are in genes like in BRCA1 and BRCA2, where we don’t have anything like curative treatment. In the medium term, yes, this could be very useful, but the headline is over the top.

I had the chance to attend the Canon Media Awards Night, as a guest of the Science Media Centre (who are one of the sponsors).

It was a good year for data journalism.  Harkanwal Singh and his team won “Best use of interactive graphics” and “Best multimedia storytelling” for projects based on effective communication of publicly-available data.

Perhaps more importantly for the future, the citation for the Herald’s “Best digital cross-platform news coverage”  explicitly called out the integration of data:

“The combination of exclusive breaking stories, data journalism, use of the digital media platforms and social coverage, meant the user’s experience was both exciting and broad.”

with similar comments in the citation for best website.

Bloggers can do data analysis and visualisation. What the professional media can do that we usually can’t is combine this with traditional reporting — stories of individual experience, or detailed investigation of who is hiding what and why.

For the consumer of traditional journalism, data literacy gives context — is this the tip of the iceberg or just the tip of the icecube? Interactive, visual data publishing adds the opportunity for readers to explore further and have deeper engagement with the story.

• Sometimes people with an axe to grind are right. In this case the people who cast aspersions on the leading data-based research opposing same-sex parenting. The closer they look at the data, the less convincing it is. (NY Magazine, new research paper) “The reanalysis illustrates the importance of methodological decisions in research”
• A study of spreadsheets in their natural habitat: blog post, paper by Felienne Harmans
• Facetted barcharts and fluctuation diagrams, from Di Cook. The data describes the responses of couples on questions about their sex life.
• Looking at scientists giving advice on politically controversial topics: a case study of badger culling in the UK by Helen Briggs. “The badgers moved the goalposts”
• From the New Zealand conference ‘Going Public,’ on the same topic, a post by Dr SM Morgan , who works on health literacy. “Find something complementary to say about a scientific colleague’s scicomm efforts and imagine saying it out loud to their face.”

Q: Why does Stuff think playing ‘Call of Duty’ increases the risk of Alzheimer’s disease? I didn’t think old people played violent video games much.

A: I don’t think Stuff does think anything in particular about it. They just reprinted that from the Telegraph and trimmed out the casual sexism.

Q: Ok, why does the Telegraph think playing ‘Call of Duty’ increases the risk of Alzheimer’s disease? I didn’t think old people played violent video games much.

A: It’s not so much about the games they play now as the ones they played 60 years earlier

Q: What video games did they play 60 years ago?

A: Not current people with Alzheimer’s; gamers now who might get Alzheimer’s in a few decades.

Q: Ok, so why will that happen?

A: Because video game players use response learning strategies for navigation in video mazes

Q: Why is that bad?

A: Because other research found people who used those strategies had more activity in their caudate nucleus.

Q: Is this going to start making sense soon?

A:. Yes. Sorry. The research found that when navigating a virtual-reality maze habitual game players used strategies that had previously been correlated with less activity in a part of the brain involved in memory and spatial awareness than normal people did. They apparently used different strategies involving other parts of the brain.

Q: And why is this a problem?

A: Because that part of the brain, the hippocampus, is less active in people with Alzheimer’s, as well as some other neurological and psychological disorders

Q: While they’re playing video games?

A: No, all the time.

Q: Couldn’t it just be that the video gamers have developed a more efficient strategy and that their hippocampuses are perfectly fine. Or hippocampi, whatever?

A: Yes, that could also be the case.

Q: I mean, if you saw people twitching their thumbs rapidly playing a video game it would be fine, but if they were just doing that while sitting around at meetings you’d worry a bit.

A: Indeed.

Q: Did the research look at memory or cognition at all?

A: No.

Q: Do they even know that these brain differences happened after playing video games? Could it be that people who don’t use that part of the brain for video navigation are just better at games?

A: It could be, yes.

Q: The story quotes the percentages using the parts of their brain to four significant digits. Does that mean there were tens of thousands of people in the research?

A: No.

Q: How many?

A: 59: about 30 in each group

Q: If this was true, could it explain why dementia is increasingly common?

A: No.

Q: Why not?

A: Partly because it’s too soon, and partly because dementia isn’t increasingly common at a given age, at least in the US and Europe. If anything, it’s less common. There are more cases now because there are more old people.

Q: It sounds like more research might be needed before writing international headlines about the risk of a terrifying disease.

A: You think?

Team Ratings for Round 11

The basic method is described on my Department home page.

Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Performance So Far

So far there have been 80 matches played, 44 of which were correctly predicted, a success rate of 55%.

Here are the predictions for last week’s games.

Predictions for Round 11

Here are the predictions for Round 11. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.