When I cite a news article, I almost never cite The New York Times. There is a reason for this. The reason is that New York Times articles are long, detailed, well written - and carefully crafted to present only one side of the story. In more plebeian sources, one sidedness is often easily detected, but in the New York Times, the level of detail and the writing skill are very effective in lulling the reader into thinking they are getting the whole story - when in fact they are getting only half the story, if that.
The most recent New York Times article I read, forwarded by a good friend, is a case in point. The article is on the finding of Denisovan DNA in 400,000 year old femurs in Spain, previously thought to be from ancestors of Neanderthals. Since the DNA is Denisovan rather than Neanderthal, they conclude that the fossils, instead of coming from a Neanderthal ancestor, instead indicate that Neanderthals later replaced the preexisting population of Denisovans. It's a pretty convincing argument, if all you read is that article from The New York Times.
The problem is, if you go back to the actual papers, the DNA in question is mitochondrial DNA. Mitochondrial DNA is inherited only from the mother, and is not subject to the recombinatorial mixing that happens with nuclear DNA. As a result, mitochondrial lineages regularly disappear from populations, when females have only male children. However, the females are still ancestors of their grandchildren through those male children, even though those grandchildren don't have their mitochondrial DNA. That means that, contrary to the conclusions of The New York Times, the Spanish fossils with Denisovan mitochondrial DNA could easily still be from the ancestors of the Neanderthals in that area.
Excessive confidence in mitochondrial DNA was responsible for one of the greatest errors in archeology - the "recent African replacement" hypothesis that modern humans' ancestors emigrated from African within the last 200,000 years, and replaced all nonafrican archaic humanoids without interbreeding. Nuclear DNA has since shown that most humans actually have some Neanderthal DNA, proving there was significant interbreeding, and that some of our ancestors from 200,000 years ago were from Europe or Asia rather than Africa.
Given that the recent African replacement hypothesis so spectacularly failed due to overreliance on mitochondrial DNA, you'd think that a moderately long article - about 1500 words - would spend at least a paragraph or two on the issue. But no, the paper that trademarked "all the news that's fit to print" ignores perhaps the most important point in the scientific finding, and doesn't use the word "mitochondrial" even once in those 1500 words.
Why doesn't The New York Times mention this key fact? Well, part of the reason may be that the idea that Neanderthals unexpectedly replaced a previous population in Spain may sell more papers than a more objective article; newspapers are to a large extent entertainment these days, just as television news is. But, another part of the reason may be that The New York Times was a big backer of the recent African replacement model for reasons of political correctness - it was an afrocentric model, and arguably feminist due to the idea of "mitochondrial Eve" - and are still trying to preserve their leftist myths instead of publicizing facts that are less politically correct.
If The New York Times is willing to distort relatively noncontroversial science articles this badly, one can only imagine what is missing from more clearly political articles.
The New York Times article on Sima de los Huesos DNA:
Other sources accurately report the DNA as mitochondrial, and avoid the all or some of the unjustified conclusions drawn by The New York Times.
Anthropology blog with a good discussion of the actual scientific implications of the finding: