Monday, July 30, 2007

Metagenomics Based Discovery Highlight: Novel Photosynthetic Organism Discovered

Normally I avoid writing about discoveries in non Open Access journals. But I cannot help myself here. On Friday a wickedly cool paper was published in a journal that I will not name here. In this paper they describe a new bacterium: "Candidatus Chloracidobacterium thermophilum." It is REALLY rare for a new bacteria to be described in a journal like this one. How did they get it in this journal? Well this organism represents the first new photosynthetic lineage of organisms discovered in many many many years. The bacterium is in the phylum Acidobacteria and can carry out aerobic photosynthesis. Prior to this discovery, photosynthesis was only known in five evolutionary lineages - all of them bacteria: Cyanobacteria, Chlorobi, Chloroflexi, Proteobacteria and Firmicutes. Photosynthesis in plants, algae and other eukaryotes all came from symbioses with cyanobacteria to these five groups represented the only "primary" photosynthetic lineages. Thus it is a big deal to find a sixth lineage having photosynthesis.

And - here is the fun part. How did they find this? With the help of metagenomics.

Only five bacterial phyla with members capable of chlorophyll (Chl)–based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)–synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. "Candidatus Chloracidobacterium thermophilum" is a BChl-producing member of the poorly characterized phylum Acidobacteria.
That is, they saw the first hints of this through analysis of metagenomic data which was generated by isolating DNA from a Yellowstone hot spring and sequencing the snot out of it. Anyway - as some might have guessed - my only lament about this paper is that it is in a non Open Access journal (I tried to convince the lead author to submit elsewhere but was not convincing enough I guess). It really is too bad - it would be nice to post some of their figures here for others to look at and it this paper would make a great one to use for educating the public about metagenomics. But alas the public cannot get this from Science for at least 1 year and bloggers and other news sources cannot really run with the story because of the copyright limitations. So - great science and great example of the power of metagenomics but restricted public use.


  1. Why do open source advocates ignore the existence of fair use laws? Is it that they don't fit well with their agenda?

  2. Yes, OK fair use might allow people to use a figure or two from a paper. But where do you draw the line? Can I use all of their figures? I do not think so. Can I use two? Probably. What about three?

    I do not want to consult a lawyer when I write my blog. It is simply easier to not put any figures from copyrighted papers in the blog. Sometimes, I put links to figures from other sites, but if people do not have a subscription to the site, they will not see the figures.

    Here is what Blogger, which provides me this blog site for free says:

    "Before you put an image in your blog, realize that some images are protected as intellectual property through copyright. This means that the creator has sole legal rights to their works and may not want you copying and displaying them. If you are unsure whether or not an image is copyrighted, it's best not to risk it."

    Since I do not want to viol.ate copyright and since I do not want to lead to grief for Blogger, I always avoid copying figures from elsewhere. As I said above, sometimes I put links to others images but am pretty careful about that most of the time and rarely if ever post links to images that are on restricted access sites.

    Of course, at least I am open about my agenda and do not hide behind anonymous commentaries.

    Unfortunately fair use is open to interpretation. And if you do not want to have to consult a lawyer about your blog, it is best to avoid using copyrighted figures from other people as much as possible.

  3. Oh and by the way, unlike some others who support Open Access, I do not believe copyright is per se a bad thing. I think it has many many positive uses. And thus I try to avoid violating it. But I do believe that scientific research funded by the government, especially primary research which describes new discoveries, should be published in as Open a manner as possible in order to get the most public benefit out of it. I think it is fine for commentaries, news, reviews, etc to be kept as non OA for some period of time (e.g., as is done by Biomed Central to generate revenue). That does not mean that it would not also be beneficial to have OA reviews but I accept that we need to be creative about finding ways to incentivize journals to provide the research in an OA manner. And we also need ways to incentivize publishers to do development work and editing to spread knowledge. I just think that putting roadblocks in place for the research results is a bad thing.


Storify of Day 1 of "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was...