While the science community reacted with indignation and shock this week over ScienceBlogs' decision to publish a blog on nutrition written by food giant PepsiCo, I was unsurprised. I've been here before with Seed magazine, owners of the ScienceBlogs network.

Yesterday, no doubt in response to the loss of some of its star bloggers, the offending blog, Food Frontiers, was removed. Adam Bly, founder and chief executive of Seed Media Group, apologised to his community for "what some of you viewed as a violation of your immense trust in ScienceBlogs. Although we (and many of you) believe strongly in the need to engage industry in pursuit of science-driven social change, this was clearly not the right way."

ScienceBlogs rightly prides itself on hosting the insightful and often amusing observations of some of the world's top scientific minds. Some ScienceBloggers feared that Food Frontiers, which was written by scientists under contract with Pepsi, would not feature honest, independent blogging. They began to leave the site in protest.

Seed would have received welcome advertising funds by blurring its content in this way, but would this have been enough to compensate for the blow to its reputation?

As far as I am concerned, the company no longer had a reputation to uphold. Until last year, I wrote a regular column for Seed. In fact, I will always be grateful to them for backing my plans to travel through developing countries looking at the influence of science on development, the effects of climate change and related issues that other media often shy away from.

However, things went pear-shaped pretty early in our relationship. Seed had published six of my columns before I realised things weren't as they should be.

I had sent them my next couple of columns: a news story from the Maldives announcing a new ban on whale shark hunting, and a column written in February 2009, from Bhopal, India, 25 years after the chemical explosion there. I heard nothing for a few weeks, by which time the whale shark piece was "old news" in journalism terms.

Then, after sending Seed requests for payment, I received an email from my editor asking for more columns and explaining that they wouldn't be publishing the Bhopal piece because it was critical of Dow Chemical, which now owns the company that caused the gas leak in 1984, and that Seed was seeking an advertising contract with Dow.

The email said:



We're not running the bhopal piece, and we're passing on the Maldive shark ban (a bit late now... Too bad it got caught up in prod week... ). As for Bhopal, it's a cautionary call on our part as we're in the midst of advertising negotiations with Dow (who have been inspired by Seed's photography in their own brand campaigns). RE: the payment, as you're on a scheduled direct-payment, the bhopal fee covers the Kerry/Carbon trading news piece fee that was outstanding. Let me know if that's clear.

Crystal clear. It seems I had to run my articles past the ads department. In more than a decade working in the industry, I had never come across such a blatant disregard for editorial independence.

My motivation for telling this tale is that some people think that the ScienceBlogs fiasco has been a lot of fuss about nothing – that Seed is just trying to make a buck and went about it in a rather naive way, and the scientists who left the site are blowing the whole thing out of proportion.

Freelancing, as I have discovered (and after years of being an editor), is a vulnerable occupation and it can be almost impossible to earn enough to get by. Those who left the security of ScienceBlogs may not have jeopardised their entire earnings, but it was a brave decision and they were right to take it.

Journalism is a small, inter-dependent industry. Science journalism, like every specialism, operates in a particularly small world and I know that by telling this story, my colleagues may close ranks behind Seed. But in return for all the times we journalists ask others to blow the whistle and expose corruption, I know I must be willing to do the same.

I sent the Bhopal piece to the BBC, who know the difference between editorial and advertising content. I have not been able to replace my regular column with Seed.

Gaia Vince is a freelance journalist, reporting on the human impacts of climate change