How scientific is the news?

http://www.nature.com/nature/journal/v435/n7038/full/435041a.html

The research article linked to my previous article is a primary research article. I found that the researchers tested the plant by taking off the perch and learned that this did not affect seed development. However, female plants with removed perches generated 47% less seeds than the flowers with perches. They did find that the removal of this perch did not completely affect how many birds visited the plant, though the specific birds did prefer the plants that had the perches. After more research, they found that more males visited the plants with the perch present than females, and that time spent feeding with the perch present was much longer than with the perch missing. Without the perch, plants had an increase in self-fertilization by 35%. The information given from the news story indicated that the perch had only evolved for the use of birds using it while feeding. The research article also claimed that the perch affected seed generation, and only really affected the males in use of the perch. Although the perch certainly helped, it is not as important as presented in the news article.

http://onlinelibrary.wiley.com/doi/10.1002/mnfr.201100185/full

This research article is a primary source article and was presented at a conference for the American Chemical Society. In comparison to the article posted at Science Daily, this primary research article published by Dr. Hauh-Jyun Candy explains how the process of mass spectrometer can lead to determining structural characterization of the analysed DNA adducts – DNA that is damages and causes mutations that can lead to cancer – rather than just claiming it works. It also states, however that contrary to the article which states that the number of DNA adducts can determine the possibility of cancer, with a detection limit of 1 adduct per 10 to the power of 12 unmodified DNA bases, it isn’t a very accurate source for carcinogen testing. Also, what the public news article fails to mention is that there is more than one method to testing for DNA adducts. In Dr. Chen’s research article, it is clearly illustrated that not only can DNA adducts be tested with a mass spectrometer, they can also be analysed by using a method called P-postlabeling, which is not mentioned in the Science Daily article. This second method of offers another approach to analysing DNA adducts, giving the proposition of testing for carcinogens in saliva more credibility. However, this method also has a poor labeling efficiency and recovery period as well as it a very laborious and arduous task with multiple steps. Both of these methods, although very ingenious, are still not very accurate. The information based from Dr. Chen’s paper leads the reader to believe that this is a possibility that has many problems yet to overcome whereas the article in Science Daily for the public is based purely to grab the attention of readers while blowing the entire research out of proportion.

http://www.kcl.ac.uk/newsevents/news/newsrecords/2011/08August/Tropical-coral-create-novel-sun-screens-human-use-scientists.aspx

This research article is a primary source article, which is presented on the King’s College Website, the institution that the head researcher, Dr. Paul Long, belongs to. The article is similar to the newspaper article I found before; however, the primary source article includes a video clip with an original interview with Dr. Long where he explains more detailed data obtained through research which was not mentioned in the news article. I found that the researchers acquired sample corals by diving into deep waters of the Great Barrier Reef, and they are presently trying to recreate a similar compound in labs through genetic engineering. Moreover, Dr. Long specifically states in the interview that the future plan is to sample their biosynthetically made compound on skin modules before testing on humans to see their effectiveness; however, the news article only mentions that a similar compound will be made in a lab which only provides a rough general idea. Furthermore, not enough emphasis was stressed in the news article about the research program’s ultimate goal which is to apply the same compound to agriculture which suffers from UV rays, and also to corals that are suffering from coral bleaching. The research article explains that the coral reef is the source of greatest biodiversity; hence, more new medicines in the future may be created by basing them upon organisms in the coral reef. Through the primary source research article, the importance of the coral reef was highly emphasized compared to the new article as it highlighted numerous different ways it can be applied to improve our daily lives as well as our future.

original story: http://www.npr.org/blogs/health/2011/08/26/139967220/vitamin-a-supplements-save-kids-lives-researchers-say

scientific article (the source):
http://www.bmj.com/content/343/bmj.d5094

The scientific article that discusses whether vitamin A supplements reduce mortality and morbidity in young children is a review article and meta-analysis where two reviewers independently chose the studies evaluated.

The interesting twist to the original news article is that it highlights how the source declares that vitamin A supplements are so undeniably beneficial, no further tests could be done ethically. While the scientific article is cited accurately, the article’s conclusion also states that studies on dosages and delivery mechanisms should be done. NPR ignores this recommendation likely to generate a more compelling introduction. The first time analyzing the story, I found that NPR’s inclusion of different perspectives on vitamin A supplements made the story more trustworthy and I doubt that anything in the story is actually false. However, NPR presented their sources to exaggerate the supposed conflict regarding the usage of vitamin A supplements. Perhaps the formal language and severe criteria for trial inclusion obfuscates some bias that a student cannot uncover, but NPR’s claim that “Other critics cite studies that show a lower reduction in child mortality from supplements” becomes not only un-cited but also untrustworthy. In the face of the scientific article’s “Independently assessed […] Randomized trials,” NPR really does look as though they are merely trying to revive the “great Vitamin A fiasco.” Latham claims that the programs get in the way of long term ways to prevent vitamin A deficiency but the scientific article agrees in that direction as well. In the paper’s subsection titled “Implications for policy,” several paragraphs are spent discussing how “Supplementation responds to an immediate need, but, in the long term, good nutrition requires reliable access to various fresh foods.” NPR’s desire to spark a debate is understandable, and even if there are differing views regarding vitamin A supplements, there is no actual conflict between the perspectives presented in NPR’s story—everyone, except some un-cited critics, agrees that vitamin A supplements saves the lives of young children, and everyone agrees that vitamin A supplements are effective but are not meant as a longterm solution.

In conclusion, a second analysis of NPR’s story following an overview of the original source reveals that the story was not actually well done at all. Instead of presenting facts as what they are NPR merely leaves a reader with seemingly conflicting views on vitamin A supplements. The story can be boiled down to two facts (and a bunch of footnotes of course).

– Vitamin A supplements are undeniably effective in reducing mortality and morbidity in young children suffering from vitamin A deficiency. (In other words, the title of the original story)
– Vitamin A supplements are a short term solution.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1706.html#/references

The journal article “Induced pluripotent stem cells from highly endangered species” was portrayed in the Scientific American as a news article. The original, scientific article is a primary research article based on the work of stem-cell biologist Jeanne F. Loring at Scripps Research Institue in La Jolla, California.
In reproducing the original article, the Scientific American kept the vital and bare-minimum details, while expanding more on the implications of the research. Although this makes for a lighter read, it didn’t quite satisfy the questions I had in the scientific process. The news article briefly touches on the process of reprogramming the genes, and thus transforming them, into the useful Induced Pluripotent Stem Cells (IPS-cells). This is only summative of the various other steps required to eventually achieve the goal of the researcher. The news article left out how they used retroviral vectors with genetic information from humans to reprogram the animal genes. There are also other useful applications of the IPS-Cells since researchers are still in the process of actually being able to use them to “rescue an endangered species”, whereas the news article only mentioned this one application. As described in the research article, there are hopes of being able to develop therapeutic applications from the IPS-Cells for other animals. However, all of this is expected from a news article aimed at the general public; the lengthy details would probably bore the average reader. What we can learn from this is that it may not be enough to just read an article from a popular news source, and that to obtain the most in-depth and scientific perspective, it is valuable to look into the primary research source.

News Article:
http://www.news-medical.net/news/20110726/Substances-found-in-cigarette-smoke-damage-blood-vessels-endothelial-cells.aspx

Scientific Article (Source):
http://cardiovascres.oxfordjournals.org/content/early/2011/06/13/cvr.cvr165

The scientific article is a primary research article. Although cigarette smoke is a well-known risk factor for the development of atherosclerosis, Dr. Bernhard and his team decided to investigate the mechanisms that link cigarette smoke with atherosclerosis.

The news story from Medical News only briefly touched on the conclusions of the study and how cigarette smoke affects the body without ever mentioning the procedures used to reach those conclusions. On the other hand, the scientific article describes those steps in great detail and as a result, ends up being far harder to understand for the average reader than the news article. The news article left out how Dr. Bernhard’s team discovered that cigarette smoke extract causes the accumulation of misfolded proteins in the endoplasmic reticulum and this eventually leads to autophagy if this effect is prolonged. The final comment in the scientific article shows that more research is needed before it can be confirmed this is the main reason cigarette smoke causes atherosclerosis and damage to endothelilal function, since it uses the words “may cause” while the news article has no such implications. Overall, the news article simplified the key points mentioned in the scientific article to attract a broader audience, but the key details in the original scientific article makes it a valuable resource for those who have a deeper interest in the subject.

http://www.sciencedirect.com/science/article/pii/S0160289611000286

IQ of a child in this article is based on SAT, ACT, a composite of the SAT and ACT exam, and the NAEP test done by high school students in the United States of America. However, the only IQ exam score taken into account of this study was the NAEP test as it gave a sample of all public school students in all 50 states. The other tests did not give a random sample as the other three tests were done by only students who planned to attend colleges and universities. The infectious diseases used in the study were only the ones available for all 50 states in the annual Morbidity and Mortality Weekly Report’s “Summary of Notifiable Diseases, United States” from the American Centers for Disease Control (CDC) for years 1993 to 2007. The results of a 15 year time-span were used. Education variables were based on student to teacher ratio and percent of teachers in public school that are “highly qualified” and wealth variable, called “state wealth” was based on a conglomeration of income per growth per capita, gross state product, and median household income. Variables excluded from the experiment was evolutionary timeline and temperature; evolutionary timeline was not included because most of the American population have not been occupying the nation for significant evolutionary changes to occur and temperature was not included because it would be controlling infectious disease across the United States nor is there an explanation of a clear relationship between intelligence and temperature found yet. The results found in the experiment showed that the variables, education and wealth, also significant influence on the average IQ of a high school student. The researchers also note that more research needs to be done to affirm their hypothesis. Therefore, the article found on Scientific America has exaggerated the claim that infectious disease is the primary variable that affects human IQ because other variables such as quality of education, student to teacher ratio and wealth also significantly affect the IQ of high school students across America.

The CNN article that I read mentioned the study from “Science” yet did not specify which article was reviewed. There were five research papers as well as a summary that presented the conclusions of the researchers with other professional opinions all in the same edition of “Science”. I cannot be sure whether the CNN reporter actually read all the primary research or the review, which was not written by any of the researchers.
I learned a lot more about how the research team came to their conclusions about the possibilities that Australopithecus sediba is an early ancestor of the Homo genus. They dated the isotopes found in the area surrounding the fossils, used x-ray microtomography to produce close-up images of the brain, and examined the bones themselves, including a pelvis, a hand, and a foot. The articles did put an emphasis on the possibility that this species may be a new link in our family tree, but it also examined ideas that I found just as compelling- such as new beliefs about why hominids evolved the way we did. For example, they may have started walking upright before their pelvises and brains enlarged, which may change the idea that the need to birth babies with larger brains was one of the factors influencing the shift to bipedalism. I think the article in CNN presented the actual debate about whether or not Au. sediba fits into the Homo genus family tree (which is presented with both options clearly explained) but did not fully report on the other interesting debates and ideas brought about by the research.

http://www.pnas.org.ezproxy.library.ubc.ca/content/108/30/12260.full.pdf+html

The primary research paper cited by the news article is titled “Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii,” which was published in the Proceedings of the National Academy of Sciences. This is the research article written by the research group from the University of Kentucky.
In the beginning, I felt that generating massive amounts of biofuel from microalgae seems a fantastical idea. After reading through the article, I found that it did a respectable job in providing a compendium of their research. Although the news article published in Nature’s Scitable blog spot used colloquial language easier to comprehend for the average person, the detailed analysis of the research paper further convinced me of the plausibility of capturing the genes encoding for the biosynthetic capacity of B. braunii and engineering this metabolism into a higher-yielding, heterologous host.

The news article reflected the ideas quite accurately, and I do not feel it exaggerated in any way. The research group was indeed drawing on applications of the hydrocarbon production of microalgae that contributed to Earth’s oil and coal shale deposits. The methods of isolation of the oil-producing genes mentioned in the news article, most notably the assessment of squalene sythase-like cDNAs for botryococcene biosynthesis using independent sequencing, were explicitly summarized in the paper. To improve the efficiency of biosynthesis, the yeast was made to over-express gene fusions of SSL-1 (squalene synthase-like gene) and SSL-3 harboring the ER membrane targeting the squalene synthase. This further supports the claims made by the news article that the mechanism can be engineered in a host.

However I do feel that the news article portrayed a more idealized and optimistic picture of the future of generating power from a renewable bio-source. The research paper was more stringent and technical in presenting their data, results, and methodologies, with a number of proposed experiments failing to yield desirable results.

http://pubs.acs.org/doi/full/10.1021/ja204775k

This primary research article published in the Journal of the American Chemical Society describes DNA probes able to monitor specific transcription factors in real-time, from enzyme function to protein shape changes. The article reiterates Science Daily’s report that previous DNA probing was “slow and cumbersome.” The writers fully explain their new method (which requires “half the sample” and “a fifth of the time” as compared to the generic approach) and mention cancer detection as a possible application of their findings. However, Science Daily’s post suggests stem cell reprogramming as well, which the original research article fails to reveal. Although this is not a far stretch, the researcher’s lack of mention raises doubts about the news article’s validity. Overall it seems Science Daily has tailored the findings well to the public eye, explaining DNA basics and inflating the significance of infamous stem cell and cancer applications as a hook.

The scientific article that was the basis for the news in The Guardian is a primary research article, where the researchers concluded from the results of their experiments that the decline in neurogenesis is due in part to blood-borne factors.

The original article in Nature goes into much greater detail on the experimental procedures, results and conclusions. It also contains several figures to aid understanding of their experiments and results. There are pictures of the mice used in the experiment, graphs of their results and a Venn diagram showing age-related plasma factors in mice. However, even with all these visual aids, the information contained in the article is not easy to process. It is clear that the original journal article’s target audience was not the general public but rather the scientific community.

The news article in The Guardian gave a highly condensed and simplified version of the results, using general terms that the public can understand. It was also slightly misleading since the simplified report on the results ended up being much less precise about the research done and more assertive about the possible benefits than the original article.

http://www.nature.com/nature/journal/v477/n7362/full/nature10358.html
The original paper that was referenced in the news article is a primary research article, since the researchers have conducted a clinical trial and found out that virus JX-594 selectively infects, replicates and expresses transgene products in cancer tissue after intravenous infusion. It was originally released on Nature, which is a well-known reliable magazine throughout the globe.

Unlike the research paper, since the article tends to be read by the educated public rather than professional scientists, the article glosses over the detailed elements of the experiment. For instance, the article insists that the virus, named JX-594, can selectively target cancer cells via bloodstreams throughout the body without mentioning that the virus is engineered. The original scientific paper explains the function of the virus JX-594 in details as the virus serves as a vehicle for the intravenous delivery and expression of transgenes in tumors. As normal tissues were not affected, the use of virus enhances the efficacy and safety of biological molecules in cancer therapy. Perhaps to arouse more interest, the title of the news article concluds that ‘anti-cancer virus’ shows promise, which exaggerate the fact. Since the scientific paper sums up that this research provides a good platform for cancer target therapy, and the platform technology opens up the possibility of future development of more specific antitumor agents and diagnosis. It is still under discovering, not showing any trace of promise. However, despite a little exaggeration, the news article in the CBC does provide a reliable, though extremely simple summary of the original scienrific article.

I was able to follow a few references through a couple articles back to the original posted on Nature by Martin Blaser, titled “Antibiotic overuse: Stop the killing of beneficial bacteria”.

http://www.nature.com/nature/journal/v476/n7361/full/476393a.html#/references

Although Blaser briefly mentions an experiment of his own in the article it is primarily a review article of various findings and trends regarding antibiotics in the past decades. Blaser summarizes multiple different studies, particularly those on relative amounts of “beneficial” bacteria in children currently compared to the past.
Although still quite generalized, the original article has more data and is considerably more accurate. I did happen to see a complete contradiction between the two articles. Blaser recommends to ” reduce the use of antibiotics during pregnancy and childhood” while the popular article says “it might be time to consider not giving antibiotics to anyone other than very young children and pregnant women”. This severely reduces the credibility of the popular article in my opinion. Also, you see much less specified language in the popular article, which refers to stomachs as “guts” and bacteria as “bugs”. There are clearly different audiences intended for each article.

Link to the paper:
http://aob.oxfordjournals.org/content/early/2011/08/10/aob.mcr172.abstract

The research paper titled “The natural history of pollination and mating in bird-populated Babiana (Iridaceae),” published in the Annals of Botany journal, was primarily a study on the fertilization methods of five species Babiana flower. This is a primary research article and presents original findings. Researchers observed that sunbirds were primary pollinators of all five species of flower, and also that all five species were capable of self-pollination, though some species could self-fertilize better than others.

The BBC news release on the study suggested that the Babiana flower had evolved a specialized bird perch in regions where bird activity was most present. In reality, it seems the researchers have related the need for the flower to evolve a specialized bird perch for pollination to certain species of the flower having a less substantial ability to self-fertilize, an important factor which was not included in the BBC article. The paper was a very long and rigorous study on numerous characteristics of these flower species, and the observation exaggerated by the BBC article (one species of Babiana had a stem length which varied geographically) was actually a very small element of a complex report.

News article: http://www.sciencedaily.com/releases/2011/09/110907132106.htm

Primary Source:
http://pubs.acs.org/doi/full/10.1021/ja204775k

The source of my news article on transcription factor-detecting nanosensors is a primary article published by researchers at UC Santa Barbara. I found the news article to be fairly accurate in representing the research: it summarizes the key points of using a DNA rather than RNA or protein probe, and the easiness of observing transcription factor activity via florescence. However, the article generalizes the applications of the research, emphasizing the implications of TF beacons in cancer treatment. The primary literature focuses on the efficiency of the TF beacon method as compared to previous technologies, with only a brief mention of drug applications in the final sentence of the paper. The primary article appears more grounded in the reality of the process – opening cancer treatment as a suggestion for future research – while the news source glorifies the effect of TF beacons on cancer detection which has not yet been explored.

(1) The scientific article is a primary research article.

(2) The findings presented in the news story summarize the research paper pretty well, including details about how there were 41 epilepsy patients tested for recording single-neuron responses in the amygdala as they viewed images of people, animals, landmarks, or objects; how the human amygdala responds preferentially to pictures of animals; how the response behaviour was only in the right and not in the left amygdala; and how this finding supports the fact that animals were a highly relevant class of stimuli during vertebrate evolution. The main difference between the news story and the original scientific article was the extra scientific detail in the methods section excluded in the news story, including how there were other neurons recorded in the hippocampus and entorhinal cortex that also responded significantly to the presented stimuli, and how they used a categorization technique that has been applied to neurons in monkey inferotemporal cortex to analyze how images are segregated by response patterns. Also, the news story mostly presented interview quotes from the researchers, which used less of the scientific jargon and were more directed towards the general public audience.