Category Archives: Research

From Ghost Writing to Ghost Management in Medical Journals

Ghost Management: How Much of the Medical Literature Is Shaped Behind the Scenes by the Pharmaceutical Industry?

As discussed below, a substantial percentage of medical journal articles (in addition to meeting presentations and other forms of publication, which are not the focus here) are ghost managed, allowing the pharmaceutical industry considerable influence on medical research, and making that research a vehicle for marketing.

Ghost writing and honorary authorship are not in and of themselves scientific problems, though they become so when they shape science to meet particular interests [1]. Some honorary authors are senior professors and chairs of departments, who are added to articles because of local academic politics rather than at the request of drug companies [15,16].
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It has been repeatedly and firmly established that pharmaceutical company funding strongly biases published results in favor of the company’s products [17–19]. Ghost management amplifies that bias, because when one set of commercial interests exerts influence at multiple stages of research, writing, and publication, it will shape the resulting article.

This PLoS published essay includes 52 citations of studies in this area.

While they are clear to distinguish drug company influence on authors and other influence, I can see no justification for honorary authorships. Why can’t people just be honest. Is that really too high an expectation for scientists? Academic politics should not trump truth – especially for scientists. I can understand that traditionally claiming authors that were not actually authors has not been uncommon. But what reason is there to be dishonest in this way now? I don’t know of a good reason. Therefore it seems to me this practice should be seen as any other dishonest practice and those interested in finding the truth should stop making dishonest claims of authorship.
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Thinking Slime Moulds

Those amazing slime moulds

In other words, science has shown how unicellular organisms like the slime mould have the ability to learn and remember. Memory and learning seem to not be limited to us humans and can be found, as expected from an evolutionary perspective across organisms.

The amoeba Physarum polycephalum is quite a performer as it has been able to navigate mazes and solve simple puzzles.
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Nakagaki, T., Yamada, H. & A. TÃ³th. “Intelligence: Maze-solving by an amoeboid organism” Nature 407, 470 (2000).

The plasmodium of the slime mould Physarum polycephalum is a large amoeba-like cell consisting of a dendritic network of tube-like structures (pseudopodia). It changes its shape as it crawls over a plain agar gel and, if food is placed at two different points, it will put out pseudopodia that connect the two food sources. Here we show that this simple organism has the ability to find the minimum-length solution between two points in a labyrinth.

What Are Slime Moulds

Members of this class are commonly referred to as slime moulds. These have thought to belong to both animal and fungi kingdoms at one time or another. It’s now known that they are quite unrelated to animals and fungi and now are classified in the Kingdom Protista.

However slime moulds do exhibit characteristics of both fungi and animals. In the feeding stage, the slime moulds moves about as a mass of protoplasm (the plasmodium) feeding on bacteria, spores, and other organic matter much like an amoeba. When the food supply is exhausted or other unfavourable conditions occur, the plasmodium changes, taking on the appearance of a fungus.

Synthesizing a Genome from Scratch

In the new study, scientists ordered 101 DNA fragments, encompassing the entire Mycoplasma genome, from commercial DNA synthesis companies. These fragments were designed so that each overlapped its neighboring sequence by a small amount; these overlapping stretches stick together, thanks to the chemical properties of DNA. Researchers then bound the fragments piece by piece, eventually generating the full 582,970 base pair Mycoplasma sequence.

New Questions on Treating Cholesterol

For decades, the theory that lowering cholesterol is always beneficial has been a core principle of cardiology. It has been accepted by doctors and used by drug makers to win quick approval for new medicines to reduce cholesterol.

But now some prominent cardiologists say the results of two recent clinical trials have raised serious questions about that theory — and the value of two widely used cholesterol-lowering medicines, Zetia and its sister drug, Vytorin.
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“The idea that you’re just going to lower LDL and people are going to get better, that’s too simplistic, much too simplistic,” said Dr. Eric J. Topol

via: The Cholesterol Mystery

Country H-index Rank for Science Publications

The SCImago Journal and Country Rank provides journal and country scientific indicators developed from the information contained in the Scopus database. As stated in previous posts these types of rankings have limitations but they are also interesting (such as the best research universities 2007). The table shows the top 6 countries by h-index and then some others I chose to list.

Country	h-index	% of World Population	% of World GDP	total Cites	% Top 500 Schools
USA	793	4.6%	27.4%	43,436,526	33%
United Kingdom	465	0.9	4.9	9,895,817	8
Germany	408	1.3	6.0	8,377,298	8
France	376	0.9	4.6	5,795,531	4
Japan	372	2.0	9.0	7,167,200	6
Canada	370	0.5	2.6	4,728,874	4
Additional countries of interest
20) China	161	20.1	5.5	1,629,993	3
20) South Korea	161	.7	1.8	1,018,532	2
24) Brazil	148	2.9	2.2	752,658	1
25) India	146	17.0	1.9	994.561	.4

Read more about the h-index (Hirsh index). Country population and GDP data taken World Development Indicators 2007, by the World Bank.

via: Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Discussing Medical Study Results

Brazilian berry destroys cancer cells in lab, UF study shows:

“Acai berries are already considered one of the richest fruit sources of antioxidants,” Talcott said. “This study was an important step toward learning what people may gain from using beverages, dietary supplements or other products made with the berries.” He cautioned that the study, funded by UF sources, was not intended to show whether compounds found in acai berries could prevent leukemia in people.

“This was only a cell-culture model and we don’t want to give anyone false hope,” Talcott said. “We are encouraged by the findings, however. Compounds that show good activity against cancer cells in a model system are most likely to have beneficial effects in our bodies.”

Other fruits, including grapes, guavas and mangoes, contain antioxidants shown to kill cancer cells in similar studies, he said. Experts are uncertain how much effect antioxidants have on cancer cells in the human body, because factors such as nutrient absorption, metabolism and the influence of other biochemical processes may influence the antioxidants’ chemical activity.

The title the University of Florida gives the press release is misleading I think (even though true). But at least the text provides reasonable caution. We really need to make sure press releases (especially from Universities) don’t focus on hype. Universities need to be held their missions of education which includes helping the public understand science not confusing the public. Dr. Talcott’s page on the AÃ§ai berry. Universities are obviously more and more focusing on revenue instead of education – I am sure they will claim to support education… but they need to show that is true.

Mapping Where Brains Store Similar Information

CMU finds human brains similarly organized

Based on how one person thinks about a hammer, a computer can identify when another person also is thinking about a hammer. It also can differentiate between items in the same category of tools, be it a hammer or screwdriver.
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The study makes two important scientific advances: “[T]here is an identifiable neural pattern associated with perception and contemplation of individual objects, and that part of the pattern is shared” by people.

The study reveals that patterns of thought extend into different regions of the brain, reflecting its complexity. It proves that a simple image can invoke thoughts in various regions of the brain, including how to use the object and experiences one has had with the object.

The study also helps to explain how the brain organizes thoughts, and the commonality of that process. “I want a complete mapping of brain states and thoughts,” Dr. Just said. “We’re taking tiny baby steps, but anything we can think about is represented in the brain.”

Robot Fly

Tinker, Tailor, Robot, Fly

Designing an automated fly implied having the ability to make lightweight, miniature working parts, a process that Wood says took up the bulk of his doctoral study, because of the lack of any previous research on which to draw. “For years, the thrust of our work was ‘How do we do this?'” says Wood. “There was no existing fabrication paradigm, given the scale we were operating on, the speed we wanted to operate with, and things like cost, turnaround, and robustness.” His research group developed and fabricated a laser carving system that could meticulously cut, shape, and bend sheets of carbon fiber and polymer – both strong but lightweight materials – into the necessary microparts.

And how to power those wings to beat 120 times per second? To keep this 60-milligram robot (the weight of a few grains of rice) with a 3-centimeter wingspan to a minimal size and weight, Wood says, you can’t simply use a shrunken version of the heavy DC (direct current) motors used in most robots. So he and his team settled on a simple actuator: in this case, a layered composite that bends when electricity is applied, thereby powering a micro-scale gearbox hooked up to the wings. Wood says the actuator works even better than its biological inspiration. The power density – a measure of power output as a function of mass – of a fly’s wing muscles is around 80 watts per kilogram; Wood’s wing design produces more than 400 watts per kilogram.

The first takeoff occurred late one evening last March, as Wood worked alone in his office, his colleagues gone for the evening. As the fly rose, Wood jumped up in celebration, quickly verified that his camera had captured the flight, and let out a sigh of relief.

Problems with Scientific Research Funding

The Wired blog proposes the following, Vote for the Biggest Problems with Scientific Research Funding

The cost of the wars in Iraq and Afghanistan, which could exceed $1.2 trillion, are particularly appalling when compared to the measly $6.43 billion requested by the National Science Foundation and $28.6 billion requested by the National Institutes of Health for supporting nationwide research in 2008.

Join us in complaining about the many problems with research funding in the voting widget below.

Some of the current leading problems: Defense Contractors Get More Tax Dollars than Medical Researchers, Keep the masses uneducated = some Republicans don’t believe in evolution, The Science of Global Warming, No Federal Funding for Embryonic Stem Cell Research. Those may or may not serious problems but they do seem to show a tendency for certain constituencies to be vocal online.

I don’t think this voting is actually very insightful. But it is at least raising two issues I have been raising a bit more lately: science funding (our newest category) and politics and science (Science and Engineering in Politics – Politics and Science Research).

New Drug Targets May Fight Tuberculosis in Novel Way

New Drug Targets May Fight Tuberculosis and Other Bacterial Infections in Novel Way

“We have developed the first inhibitor of a key small molecule from Mycobacterium tuberculosis and Mycobacterium leprae (which causes leprosy) utilized to subvert human host’s defenses and damage and invade human host’s cells during infection,” explains study senior author Dr. Luis Quadri, Associate Professor of Microbiology and Immunology at Weill Cornell.
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“We are moving beyond antimicrobials such as antibiotics, which kill the bacterium directly, to anti-infectives, that may have no effect against the pathogen in the test tube but which do compromise its ability to infect and spread in the host,” he explains. “We believe that the expansion of the drug armamentarium to include such anti-infective drugs could help the fight against multi-drug resistant infection that has become such a challenge today.”
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“I believe that drugs targeting virulence factors are just one component of the paradigm shift in the antimicrobial drug discovery for the 21st century—one that will offer patients more options in the fight against truly global killers,” he says.