What’s been going on?

It’s been a while since I’ve been able to blog.  I have lots of reasons, but one of the big ones is that I’ve been writing and editing for some other sites!

In mid-January, I wrote an article for the ISBER News Blog (ISBER stands for the International Society for Biological and Environmental Repositories – the premiere biobanking society in the world). The article entitled “Have you joined the ISBER social network? Facebook!” is all about how to get started on Facebook and how to get more involved with ISBER through that social media outlet.  If you aren’t on Facebook already, you may find the first half of the article useful.  Once you join, you can follow the “Things I Tell My Mom” Facebook page where I post often about interesting science I find around the web.

From this experience, I was named the new Assistant Editor for the ISBER News Blog. This was announced in a very funny article from the current editor Rick Michels called “Bringing in Backup.” I’m super excited about this new role and have jumped right in to help edit lots of interesting articles from the biobanking world.  I hope many of them will be interesting to the public, and I’ll be sure to share them either through this blog or on my Facebook page.

As part of my job, I endeavor to educate the public on the importance of biobanking in enabling cancer research. To both work towards this goal as well as to talk about the Biobank’s support of World Cancer Day, I wrote an article for the Barrow Neurological Institute blog about what our Biobank does to help cancer research. You can find that article here.

And because that’s not nearly enough, my first article for GotScience.org was published today. GotScience is a fabulous website with the goal of increasing the public awareness about science – a perfect fit for my goals and dreams! I adapted an article that I first published on this blog for GotScience about “What is a biobank?” (I think you can see a theme emerging). Please check it out along with the other articles on GotScience!

Finally, I’ve been helping out an editor friend of mine at PN Online – a magazine to help people who are wheelchair bound. I contributed to an article about this great new ALS research called “Early ALS Treatment.” I adapted my work for this article to a journal club blog post that you can read here.

I promise I’ll be back to writing on this blog soon, but until then, enjoy the articles I shared above!!

Sci Snippet – Do iPhones kill people?

Look at this graph. It’s incredible! As iPhone sales increase from 2007 to 2010, so did the number of deaths caused by people falling down the stairs.  They even increased at the same rate.  It’s crazy – iPhones cause people to die falling down the stairs!!

correlation-causation

For this and other hilarious graphs of silly correlations see tylervigen.com

How obviously ridiculous this is.  Most people could logically deduce that just because iPhone sales and deaths from falling down the stairs “correlate” that one does not “cause” the other. There are lots of other examples (and you can create your own silly correlations) from Spurious Correlations or on other news sites here or here.  And in these cases, you can laugh realizing that just because these two things happen together does not mean that one causes the other.

But even though you’ve probably said that “correlation doesn’t imply causation” or heard someone say it, in science (and science news reporting) the difference is critical to tease out. Why? Understanding if something in science is a cause of the effect you’re seeing can

  • Prevent something harmful from causing damage. For example knowing that smoking is a cause of lung cancer resulted in public health efforts to help people quit smoking.
  • Treat a the cause of a disease or fix the cause of the problem.  For example, knowing that the h.pylori bacteria causes gastritis and ulcers provides a method for treating ulcers by killing the h.pylori. Or if you know that factory waste being dumped into a river or lake causes animal life to die or stop procreating, you can work towards stopping the dumping to save wildlife.
  • Prepare for diseases, outbreaks of disease, or natural disasters.  If you know that earthquakes cause tsunamis, then a warning system can be developed to save people in the tsunami zone.
  • Plan ahead and discuss the possible outcomes from a particular action.  When you know that lack of water in a drought causes dry forest conditions leading to forest fires, you can plan to have greater funding available for fighting these fires in a particularly dry year.
cancer-lung

“Cancer smoking lung cancer correlation from NIH” by Sakurambo – Vectorized version of Image:Cancer smoking lung cancer correlation from NIH.png, originally published on the nih.gov website. The source page has been deleted, but an archived copy is still accessible.Own work, created in Adobe Illustrator. Licensed under Public Domain via Commons

It’s just as important though to tease out when something doesn’t cause an effect – and unfortunately many false claims and pseudoscience is based on taking correlations and touting them as causes.  So how do we figure this out?

In science, a lot of this is determined experimentally and statistically.  In statistics (of which I do not claim to be an expert, but see the links below for more details), the strength of the relationship can be calculated and the stronger the more likely that one causes the other.  The cause/effect relationship should also be tested experimentally, if possible, and the experiment should be repeated to see if the same results are obtained every time.  Without experimental or repeatable experimental results, the relationship is less likely to be causal.  Another interesting measurement is to look at the time frame – if the action takes place months, days, or years apart from the effect, you have to consider whether this would make sense or not.  In the case of smoking and lung cancer, the separation of the two events by years makes sense, but in other cases it may not.  Which also brings up the point of looking at the relationship and thinking about whether or not it makes sense or if a mechanism can be found for the cause and effect relationship.  For example, we know that smoking causes DNA mutations and inflammation which is one of the mechanisms that leads to lung cancer. Alternatively, looking at the iPhone and dying from falling down the stairs example, it’s difficult to find a mechanism that could explain this relationship.

A great description of what to look for comes from the book club book that I’ll be talking about on Thursday, “Bad Science: Quacks, Hacks, and Big Pharma Flacks” by Ben Goldacre with a quote describing evidence-based medicine:

it needs to be a strong association, which is consistent, and specific to the thing you are studying, where the putative cause comes before the supposed effect in time; ideally there should be a biological gradient, such as a dose-response effect; it should be consistent or at least not completely at odds with what is already known (because extraordinary claims require extraordinary evidence); and it should be biologically plausible

Overall, it does come down to the data and some common sense.  If there isn’t any data to support the relationship, you might just be looking at correlation and can confidently holler “iPhones do not kill people!”

To better understand the differences between correlation and causation and the math that can show which you are looking at, check out the Kahn Academy course.  Read more about this topic from Stats with Cats Blog

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Sci Snippet – How are homeopathetic “drugs” made?

I was inspired by SciBabe (FB page here) who is all about debunking pseudoscience and raging against the idiocracy of everything from anti-vaxxers to homeopathic remedies. She has eaten a “lethal dose” of homeopathic pills (video here) in an effort to prove that there are no active ingredients in these sugar pills to actually kill you.

homeopathy

By Wikidudeman (Own work) [Public domain], via Wikimedia Commons

Let’s look at the “science” of how homeopathic drugs are made (read so much more about this in the fabulous book “Bad Science: Quacks, Hacks, and Big Pharma Flacks” by Ben Goldacre). A German doctor named Samuel Hahnemann in the late 1700s decided that a substance that induced the same symptoms in a healthy person as a patient with a disease could be used to treat the disease.  No joke. This is how the theory of “like cures like” and homeopathy was born.  However, you can’t just provide the chemicals or herbs that cause these symptoms directly because this could have genuine negative effects, so you have to dilute or “potentize” the substance to make it effective.  This is done through homeopathic dilutions – and according to homeopathy, the more dilute the more powerful it becomes.  How exactly does this work? You can’t just dilute like you might normally dilute substances, you have to use a process called “succession.”  Take the substance, dilute it 1:100 in water or alcohol in a glass vessel, and shake it by ten firm strikes with a “hard but elastic object.”  What is this object?  Originally is was a wooden board covered in leather and filled with horsehair and now it can be fancy robotic machines in homeopathic medicine factories.  This is repeated at least 30 times.  At the end of this, the substance is diluted 1 to 1 followed by 60 zeros – no molecules of the original substance are left.  Then this dilution may be dehydrated into a sugar pill for ingestion.  Therefore, homeopathic remedies are essentially sugar pills. So why do some people think that homeopathy works? The placebo effect – a patient psychologically expects the drug to work so it has a positive effect.

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Sci Snippet – The bug that causes ulcers

Everyone can understand that bacteria can cause a disease through infection. Bacterial infections can cause huge inflammatory responses known as sepsis or result in a cut getting infected. But a bacterial infection causing ulcers? That seems weird.

Hpylori

H. Pylori under an electron microscope

This is a crazy story, but resulted in the 2005 Nobel Prize in Physiology and Medicine. In the 1980s, Dr. Barry Marshall found that the bacteria H. Pylori is often found in people with peptic ulcers. At this point, scientists didn’t even think that bacteria could survive in the acidic environment of the stomach, much less cause a disease. Ulcers were obviously caused by stress or spicy foods or too much acid. Dr. Marshall was convinced of his hypothesis and went to test his theory in pigs, but for some reason he wasn’t able to get the H. Pylori bacteria to infect the pigs.  So one night, he drank an entire petri dish of cultured H. Pylori. As a side note – it is NOT a good idea to do experiments on yourself because you have no idea what will happen (movies have confirmed this over and over). However, three days later, he felt nauseous, after a week he started vomiting and an endoscopy found massive inflammation indicative of gastritis, and two weeks later he started taking antibiotics for the H. Pylori infection. He  was the first to definitively prove that this bacterial infection caused gastritis. Although this particular experiment did not prove that H.Pylori caused ulcers, it’s now been shown by other researchers.

In fact, now scientists know that H. Pylori bacteria is found in the stomach of about 50% of the world’s population, but in most people it doesn’t cause much of an issue. 80% of people infected don’t have any symptoms and it may actually help protect against other diseases such as acid reflux and Barrett’s esophagus. However, of those infected, they have a 10-20% lifetime risk of developing an ulcer and a 1-2% risk of developing stomach cancer. What this means is that eliminating H. Pylori by antibiotics can help treat the ulcer, and can also decrease the risk of stomach cancer.

For more Sci Snippets, click here.

Sci Snippet – How long from eating to pooping?

Based on my two posts about poop (Facts about Poop and Fecal Transplant), I received a great question about how long it actually takes for food to pass through the gut? Although I posted my answer in the comments and on Facebook, here is the answer with a few more details in case you didn’t see it.

transit-time

Thanks to North Shore Colonics for the image

The actual time from mouth to pooping depends on a number of factors (for example, what you eat and drink), and can be a critical measure of how the bowel is functioning – because we all know that things just aren’t right if we’re constipated or have diarrhea. There are a number of ways to measure “colon transit time” or “whole gut transit time”, but the most common is having subjects swallow 20-25 radioactive markers in a pill (link to what they look like here). The poop is collected and the number of radioactive rings in the stool are counted. And just in case you’re imagining researchers poking through poop – they didn’t have to do that! Because the rings are radioactive, they can count them using an x-Ray. After 5 days, researchers found that on average 80% of these rings were expelled, and 20% were still making their way out (the journal article is here). In one study, the median whole gut transit time is 27.7 hours though in other studies they find the mean to be slightly longer at 30-40 hours. Also, in general women had longer transit times than men – maybe because women’s intestines are, on average, about 10 cm longer than men’s. As an aside, you may wonder to yourself “why are women’s intestines about 10 cm longer than men’s?”  It’s not entirely known but two prevailing theories are 1) to get around the larger female internal organs like the ovaries or 2) to absorb more nutrients during pregnancy. This transit time is also affected by race – transit time is much shorter in Chinese men and women.

As you can imagine, this is a bit of an imprecise way to measure transit times and researchers are creating new tools (like electronic wireless motility capsulesthat can more accurately track how things transit through the gut. Or you can be like my friend Sarahjane who says that she informally tracks this using one of the lowest-tech options of them all – corn!

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Sci Snippet – Who reviews papers?

ReviewingThis blog is called “Things I Tell My Mom” for a reason. These are all things that I really do talk to my Mom about.  In fact, after posting about the trials and tribulations of publishing a paper, my Mom asked who these reviewers are anyway.

Reviewers are usually (hopefully) in the same field as the researcher so they have a background knowledge that will allow them to evaluate the research carefully and thoughtfully based on what is already known in the field. The editors select several (usually 3) reviewers who each review the manuscript independently. The good news is that in an ideal world, these well-informed reviewers will be in the best position to provide the journal with insightful feedback.  The bad news is that they may like what you’re working on so much that they provide suggestions for lots of additional experiments, steal the ideas in the paper and then quickly publish them before you get a chance. Is this “scooping” ethical? Nope. Does it happen? Yup.  Often? Probably not that often.

You also have to keep in mind that the reviewers know who the authors of the paper are, but the reviewers comments are anonymous. So if you get a poor review, you don’t always know if it’s because the manuscript is terrible or if the reviewer is someone who you are competitive with professionally or don’t get along with. As my Dad aptly said, “That system sucks.” This is in part why some journal are starting to offer double blind review (described in more detail here).

Beside this apparent conflict of interest, reviewers are also active researchers and therefore super busy people. If the reviewer doesn’t take the responsibility of reviewing seriously, this can mean one of two things – it will take a lot of time for them to get to reviewing the paper (dragging out the waiting) or they will look through it quickly and provide a crappy review. Crappy reviews can reject great papers or accept terrible papers. It’s an imperfect system. Some of this imperfection is highlighted on this hilarious and depressing website S**t My Reviewers Say Tumblr.

Also, keep in mind that reviewers don’t get compensated in any way for reviewing – it’s part of a scientist’s service to the scientific community. I have been a reviewer many times, and I take the job very seriously and try my best to provide a fair, complete review in a timely manner – and I expect to receive the same when I submit manuscripts as well. This is the ideal, but not always the reality.

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