- Abstract; a short statement that outlines what the paper is about, what it found and what the conclusions are. This is a quick way to digest the papers findings. Also while lots of papers are not freely available to read (boo!) without a subscription, these always are.
- Introduction: This section lays out the case as to why the question under study needs to be studied. It also reviews the current research and sets the stage for the current research.
- Method: How the scientist/s propose to try to answer the question. This is a description of what they did and how they got their results. It is also the instructions for others to recreate the results.
- Results: The findings. What the scientists found as a result of their experiment.
- Conclusion: What these findings mean, including how much they can be applied and what research they suggest needs to be done next.
- References: A list of the other papers and books referred to in this paper so you can go and look them up. They are listed alphabetically with the surname of the scientists first then the date, then the title. If there are a lot of scientists involved it is often shortened to the name of the first scientist in the list then 'et al' for 'and the rest' added.
Got it? Good. So lets take a look at a typical paper...Exceptional record of mid-Pleistocene vertebrates helps differentiate climatic from anthropogenic ecosystem perturbations – Barnosky et al. (2004) (link from AGW Observer)
So the abstract from this is:
Mid-Pleistocene vertebrates in North America are scarce but important for recognizing the ecological effects of climatic change in the absence of humans. We report on a uniquely rich mid-Pleistocene vertebrate sequence from Porcupine Cave, Colorado, which records at least 127 species and the earliest appearances of 30 mammals and birds. By analyzing >20,000 mammal fossils in relation to modern species and independent climatic proxies, we determined how mammal communities reacted to presumed glacial–interglacial transitions between 1,000,000 and 600,000 years ago. We conclude that climatic warming primarily affected mammals of lower trophic and size categories, in contrast to documented human impacts on higher trophic and size categories historically. Despite changes in species composition and minor changes in small-mammal species richness evident at times of climatic change, overall structural stability of mammal communities persisted >600,000 years before human impacts.
So if you read this you can see that that back in the mid-Pleistocene there were lots of species around back then and as the climate changed it did impact them, but overall the communities of mammals were ok. They know this because they looked at 20,000 mammal fossils. The authors suggest that once you add human impact into the mix though - the populations do not do so well.
So how would you refute the findings of this paper? You could read it and identify flaws in the method. You could repeat the examination of the fossils to see if the classification they did were accurate. You could do your own excavations of the site to see if they missed anything. In short, you need to do your own work to counter their work. But to consider how to counter it is the wrong approach - you need to go where the data leads and this is why denailism fails, because they can't accept where the data leads.