I’m casting around for significant questions that could best be answered by content-mining the current and historical scientific literature. It’s rather like an astronomer saying: “we’ve built a better telescope; now, what shall we point it at?”. We’re developing a “contentscope” – the ability to ask any Factually based question on the current scholarly content – whether Open or Closed.
BTW you can’t do this with Google or other search engines. The queries have to be based on scientific concepts. If you are asking for “cats” in Google you’ll get the musical “Cats”, LOLCats “I can has Cheezburger?”, and masses of acronyms. Look at Wikipedia:
Science, medicine and technology[edit] [12 items for CAT, I understand 3]
- …
- Catalase, an enzyme
- Chloramphenicol acetyltransferase, an enzyme
- Computed axial tomography or CAT scan, a medical imaging X-ray technology
- …
and that doesn’t include genes called “cat”, the 3-letter oligonucleotide “CAT”, the tripeptide CAT (cysteinyl-alanyl-threonine) and many more. So we have to use The Content Mine + AMI.
So here’s my question:
“Do secondary metabolites show the same process of evolution as organisms and their genes?”
I have no ideas whether this has been already answered. I wouldn’t know how or where to look. I’ll explain.
Organisms manufacture thousands of chemicals for a wide range of purposes. Primary metabolites are ” metabolites that [are] directly involved in normal growth, development, and reproduction.” Typical examples are glucose, ATP, carbon dioxide, whereas Secondary metabolites are
“… organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism.[1] Unlike primary metabolites, absence of secondary metabolites does not result in immediate death, but rather in long-term impairment of the organism’s survivability, fecundity, or aesthetics, or perhaps in no significant change at all. Secondary metabolites are often restricted to a narrow set of species within a phylogenetic group.[2] Secondary metabolites often play an important role in plant defense against herbivory[3] and other interspecies defenses.[4]Humans use secondary metabolites as medicines, flavorings, and recreational drugs.
Examples are caffeine, penicillin, thymol, geraniol. There are hundreds of thousands – plants are particularly versatile. Insects use them for communication (pheromones) to signal between individuals and groups. Plants use the to kill or deter predators. The evolutionary pressure must be considerable – if you give off a chemical signal that allows you to find a mate kilometres away (like the Gypsy Moth) you will reproduce better. If your odour can be detected by a predator then you may be in danger; conversely smelling predators is an escape strategy.
For the last 30 years I have been working in chemical similarity – here’s an example from Open Access J.Cheminf (BMC, http://www.jcheminf.com/content/4/1/28 ) – I am on the editorial board – and this is from the Pubchem group.
Here’s a simple example of similarity between chemicals. The methods are complex, but the result is essentially the same sort of tree that we use to classify species.
So maybe we can correlate exact species and its pheromones. The closer the species, the closer the pheromones. It’s easy to cluster species – go to Genbank and extract the sequences and compute the alignment and the differences…
.. and chemicals? What we want is a list of species and their associated pheromones. Some of that will be in Chemical Abstracts – no idea how much. So just write to the American Chemical Society and ask if you can download and use Chemical Abstracts for free and republish the results…
No. In any case it’s better to use the primary literature. So we can search for all papers than contain chemical compounds and also contain species. Here’s an example about the Gypsy Moth (Lymantria dispar) and its pheromone (which can be used to lure it into a trap). http://www.pnas.org/content/100/3/809.full (free but not Open). One compound is “18-methyl-nonadecanoic acid” – you don’t know what that is? Just go to http://opsin.ch.cam.ac.uk and type in in and you get:
How similar is this to other insect pheromones? We can now start to extract the raw data from the literature LEGALLY and we have a whole new tool to answer research questions. (The question isn’t “theoretical” – insect and other arthropods do vast amounts of good and vast amounts of harm and understanding their evolution and chemistry is essential).
So we’d like your help. In communal projects you don’t have to be an expert in everything.