Why most published research findings are false

So this was an interesting article published in PLoS Medicine by John P. A. Ioannidis. The article lists several reasons of why research is probably false. He argued that the smaller the sample size of your study, the less likely it is that your findings were true. Also, the number of previous studies on related work, the flexibility in the methods, the type of analysis, and the undeclared competing interests all have effects on the probability that a finding is true.

Most of what he said made perfect sense. If you have a study with only seven samples, the likelihood of the samples representing the entire population is fairly small. If you do a study with thousands of samples, your findings have more weight in their statistical significance.

There were several parts of the paper that were frustrating. For example, he didn't seem to have that many suggestions about how scientists can fix this problem. He also thinks that we should declare conflicts of interest much more, which everyone is trying to find significant results so that they can publish and earn more money, be more recognized, get that tenure, or just validate that you are spending all of your time on something significant. No one really goes into research thinking that they aren't going to find anything, otherwise, why would you study it?

He thought that flexibility in methodology makes your results invalid, I think flexibility is what makes your experiment real. Statistics works with theoretically, what is the mathematically perfect way to do this. Reality doesn't work so neat. Cell transformations have a tried and true methodology. And yet, why do so many people have difficulty transforming cells? This is due to the randomness of nature, and the fact that we are dealing with living organisms who react differently to things.

When I first read the article, I freaked out and thought, "So, my entire career is just worthless because most of my findings are probably false?!?" I feel that if so much was actually false, then it wouldn't be repeatable, we wouldn't be able to build off of it, it would appear to be flawed or fall apart. I think this paper is good to remind us that we should be careful and aim to be unbiased and as accurate as possible.

Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children

So, this past week, we read the infamously retracted paper written by A. J. Wakefield. I am going to only attribute the article to Wakefield, even though the paper was originally published with multiple authors, because all of the other authors retracted their names after they discovered Wakefield had a conflict of interest when writing this paper.
This is the article that lead to the whole "Vaccines cause Autism". There is a lot of interesting things wrong with this paper and interesting reviews of this paper. One of the main problems is that Wakefield was payed (I believe in the forms of grants) by a law firm that was planning on suing the vaccination companies. Other problems with the paper include that a bunch of the results were falsely reported, the children were never actually psychologically tested for the study to see if they had developmental disorders, and that the mothers reported the possible link between vaccination and developmental disorders.

The thing that I found most intriguing about this paper was that in the third to last paragraph the paper states, "Published evidence is inadequate to show whether there is a change in incidence or a link to the measles, mumps, and rubella vaccine." The last paragraph then goes on to state, "In most cases, onset of symptoms was after measles, mumps, and rubella immunization. Further investigations are needed to examine this syndrome and its possible relation to the vaccine." As part of the falsifying of data, if you look in the paper, some of the children started showing symptoms before they were vaccinated, and for the rest, I am going to assume that the symptoms just didn't exhibit themselves until after vaccination. This is probably due to children being incredibly young when they are immunized and don't develop the ability to talk and walk and read until they are older than that.

One of the most interesting results of this paper, was the decrease in parents having their children vaccinated. There has also been a huge increase in the amount of children catching these diseases. I think that someone should do a study comparing the number of incidents of the diseases and the percentage of children vaccinated, before this paper was published and after this paper was published. This resulting study would have a very strong correlation between children getting these diseases and children not getting vaccinated. (This study would have to take into account that if someone is unvaccinated, then there is a greater chance of the people they associate with getting the disease, even if the associates were vaccinated.)

I think one of the worst outcomes of this paper is the lack of funding that autism has now received. The general public is still under the assumption that vaccinations cause autism, so clearly they don't need to fund autism research if they already know the cause, right? Wrong.

I also thought it was interesting the amount of the paper that focused on the digestive problems of the children. I was previously unaware that children with autism tended to have digestive problems. I thought it was interesting that the children actually had colonoscopies. This was later (according to wikipedia) was considered, during the investigation of Wakefield's study, to be "unnecessary invasive medical procedures."

All in all, a very interesting study to read and research the results of.

A Pseudomonas aeruginosa Toxin that Hijacks the Host Ubiquitin Proteolytic System

So this article was pretty cool. It was published in PLoS Pathogens and written by Bomberger et al. So often in people with respiratory infections, the Pseudomonas aeruginosa bacteria can also be found in the lungs of the infected patients. This bacteria secretes a toxin known as Cif. This toxin is known for decreasing the membrane expression of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR). CFTR is a giant protein channel that helps in releasing chloride out of the cell. This facilitates in the clearing of mucus from the airways and causing an immune response. The CFTR goes through a recycling process in which it gets tagged with ubiquitin, removed from the membrane, then either A) deubiquitinated and the protein returns to the membrane or B) the protein gets sent to a lysosome and then degraded.

The toxin Cif enters the host cell, and binds to USP10 (this is the protein within the cell which deubiquitinates the CFTR so that it can then be recycled back to the membrane). The binding of USP10 and Cif then disrupts the deubiquitination process so that CFTR remains ubuitinized. This is a very neat mechanism. It seems very simple, all the bacteria needs is to release a chemical, and have it bind within the host cell, and then the host cell is unable to clear the mucus from the airways, and the bacteria retains its nice environment to grow in.

Previously, this group had studied that USP10 deubiquitinates CFTR which decreases the amount of CFTR found in the membrane. They had not studied before how the Cif toxin plays a role in this pathway. I am always amazed at how a research group just whittles away and whittles away until the entire pathway is discovered.

Furthermore, the group showed that with the USP10 protein, it is specifically the Ras-GAP SH3 domain binding protein-1 (G3BP1) that binds in the presence of Cif. The presence of the Cif toxin was shown to both increase the binding of G3BP1 to USP10 and to decrease the interaction between USP10 and CFTR. So the authors not only discovered the pathway, but figured out the specific proteins and domains (at least on the USP10 protein) in which the interactions occur.

The paper had an incredible number of figures, that showed evidence for their conclusions. I thought it was a nicely written paper and that the figure of the mechanism was incredibly helpful.

The virophage as a unique parasite of the giant mimivirus

We just read an article from Nature by Scola et al. Viruses have always presented a problem to scientists. Are they alive? I was taught back in middle school, that no they are not, but that they are that gray area between the black and white. Biologists generally define a living organism as having the ability to grow, adapt, respond to stimuli, reproduce, maintain homeostasis, metabolize, and have an organized structure. Viruses tend to meet most of the requirements but can't reproduce by themselves without a host. So most biologists don't consider them to really be alive.

The authors of this paper have discovered a virus, they named it Sputnik, that will attack other viruses. They have termed it a virophage. The virus it was attacking was the Acanthamoaeba polyphaga mimivirus, the largest known virus. The combination of the two viruses, they referred to as a mamavirus (originally they thought this was a new virus). The mamavirus was found within an amoeba. Sputnik then proceeded to rapidly grow inside the amoeba, within the viral factory. The growth of Sputnik appeared harmful to the mimivirus. The presence of Sputnik cause abnormal mimiviruses with thicker capsid layers, sometimes accumulating at one side of the mimivirus.

Sputnik appeared to decrease the amount of mimivirus growth and the killing of the amoeba. This appears to the authors as a virus (the mimirirus) that is “sick” (infected with Sputnik). This leads to questions like, if a virus can get “sick” then does this mean that it is alive? Can something get sick if it cannot reproduce by itself (and is thus not alive)? Do we now have to change our definition of living?

Another interesting thing that they have found, is that Sputnik contains genes that appear to be linked to viruses that can affect all domains of life. This leads us to conclusions that Sputnik is derived from an ancestral organism from back before the domains separated into their three catagories.

I was mostly confused while reading this paper as to the distinction between mamivirus, mimivirus, and all of the other organisms that had homologues of genes found within Sputnik. Looking back over the paper, the mamavirus appears to be related to the mimivirus, they are not the same thing.

It would be interesting to see what the effects of this paper and organism will have on science. I wonder if this will revolutionize virology (at least) and possibly the rest of biology.

Seeing with my ears!

So this past week we read "Functional specialization for auditory--spatial processing in the occipital cortex of congenitally blind humans" by Collignon et al published in the Proceedings of the National Academy of Science.

This was a very cool paper. They took eleven congenitally blind and eleven sighted individuals. They blindfolded the subjects, put them in an MRI machine, and played auditory signals at them from various locations around their head. The subjects had to push buttons indicating whether the sound was of a higher or lower pitch from the previous sound or whether the sound was more to the right or left than the previous sound. The MRI would show which parts of the brain were being used during the various tests.

The paper showed that the parts of the brain generally known as the "visual cortex" would light up in the congenitally blind during the experiment regarding location (not the one regarding pitch). These parts did not light up in the sighted individuals, in fact, they had "negative activity" (we believe that this is in comparison to activity in the rest of the brain).

The main point of this article is working to reorganize the way we think about the brain. Previously we had labeled things by what they gain input from, ie. the visual cortex, the auditory cortex. This paper is showing that instead of the important thing about x part of the brain is the function that it performs, not what its input is. This makes a huge amount of sense to me. The parts of the brain used for motor activity will take input from the eyes to figure out where your body is in relation to what it wants to be doing. But if the brain does not have visual input to work with, then it will use auditory input to help figure out where your body is spatially. WHOAH! This is something that I feel like it should have been obvious, but is in reality, probably changing how we look at the brain.

I think it would be awesome to test this out with various sensory disorders. See if there is someone who can't smell, for example, and see what parts of the brain light up when accessing memories or while they are eating. Alternatively, trying this experiment with someone who is congenitally deaf and see if their auditory cortex gets input from their eyes.

The Causes of Anxiety

Last week, we read a paper published in Nature entitled "Amygdala circuitry mediating reversible and bidirectional control of anxiety" by Tye et al. I must confess that I understood little to none of the paper upon reading it the first time. After discussing the paper as a group, I believe that I have somewhat of a better understanding, although I would not take my word on this interpretation.

Anxiety and fear are two closely related responses, although fear, I believe, is better understood. This experiment was looking at the neural pathways that control anxiety in the amygdala.
So for part of the experiment, mice were injected with a virus that affected their basolateral amygdala, and then a light was shone onto certain parts of the amygdala to induce an anxious reaction. Once the neurons were unstimulated by the light, then the anxious reaction stopped.

The anxious reactions were tested by comparing the amount of time a mouse spent on a "maze" with no sides (so the mouse could easily fall off) versus the amount of time the mouse spent in the rest of the maze that had sides. The other test was an "open field test" where the mouse was in a big room with walls and the time was compared of how long the mouse spent around the outside of the room versus the how long the mouse was in the middle of the room. I believe another test they performed was with the light in the room on versus off for both the open field test and the maze. (The light on and off might have just been referring to the stimulation of the amygdala using light, I wasn't entire sure about this).

These tests made a lot of sense to me since mice are nocturnal, prey creatures. As a mouse, you don't want to be seen, you prefer corners and places with shadow where you can hide, and you don't like light, that exposes you.

From what I could tell, this experiment was highly successful in showing which neural pathways are associated with anxiety. This will be highly useful in the discovery of new ways to treat anxiety-like disorders.

Nanodiamonds

So in class we just read a paper entitled "Nanodiamond Therapeutic Delivery Agents Mediate Enhanced Chemoresistant Tumor Treatment" by Chow et al. (2011). This paper was pretty hard for me to read since so much of it seemed to consist of methods or results from treatments that looked similar to me. The basic gist is that during chemotherapy, the drugs that are added into your system get rejected by your body. This is one of the major problems with chemotherapy, since if your cells aren't getting the drugs, then it doesn't matter how effective the drugs are.

With the nanodiamonds, the drug will bind to the crystal, and then the diamond itself can get inside of the cells, which greatly increases the rate of success.

While I feel like I should be discussing this paper in a more scholarly manner. All that this article reminds me of is the book Diamond Age by Neil Stephenson. One of the main concepts in this book that blew my mind was that everything was nano. How you attacked people, and also how you cured people was through nanotechnology.

I really think that this technology is the direction that medicine is headed in. It will start with personalized medicine, and finding ways to make that cheaper and more accessible. Sending small tiny particles seems terrifying to me, although for medicine this is an amazing discovery. I do believe that the main thing about this that seems scary is that it contains the word "nano" which I associate with nanobots. The thought of having little tiny robots inside of me seems almost like an invasion of privacy on such a basic level. Even though the nano particles are not recording anything or really doing anything related to privacy, except I guess for being inside of my person.

One of the silly things about this article is how amazing it sounds. For almost all of the article, I was thinking, what's the catch? This sounds too good to be true. The main problem is that this has only been tested on mice. The crazy part is that this is about chemotherapy. Half of chemotherapy right now is that you are poisoning your body in the hope that the tumor cells die and enough of the rest of you stays alive. Almost any sort of medicine that we can discover at this point that is slightly less toxic or that has slightly better results, we should be implementing to try and make as many baby steps as quickly as we possibly can.

I hope that this technology translates over to humans, and that not only our treatments improve but also our research into preventing cancer.

awesome t-shirt

So my boyfriend showed me this.

T-shirt picture

I love it when people indulge me in my DNA geekiness.