Tag: ScienceEveryday

The value of p

In biomedical research statistics are a funny thing. The post below touches on some of them. One thing that I’ve found that is bad but not necessarily fraud, is that many researchers learn a statistical method from a mentor or journal and use only that method, e.g., Student t-test. A t-test is perfectly fine when comparing two groups. If you have more than two groups, you have to switch to an analysis of variance, ANOVA or something else. In some fields and journals, the problem is bad enough that even reviewers don’t catch the statistical flaw. However, all is not doom and gloom. Many if not all universities have a group of statisticians on hand to help you design your study, i.e., statistical method, before you do the research. Many large grants want evidence of this, e.g. in a power calculation.

Here are a few older posts on statistics.

Beer + statistics (science) + history, FTW.

http://goo.gl/EC0Y37

Analysis of Meta-analysis

http://goo.gl/SGAmAu

Bad science → bad headlines

http://goo.gl/ojW213

Here are some examples of publications that don’t quite understand what significance means. http://goo.gl/AgWTRl

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Originally shared by Joerg Fliege

A peculiar prevalence of p-values

Now whats a p-value?  In laymans terms, it is a number saying that a particular hypothesis (“All sheeps are black”, “All math teachers are jerks”, “Aspirin helps against cancer”, etc) is not completely bats… crazy.  It roughly goes like this. You make up a hypothesis (see above) that you really do not like, and you gather some data (e.g. some sheep, or some math teachers). The p-value corresponding to this hypothesis and this data set then tells you how probable it is to randomly stumble upon that particular data set under the assumption that the hypothesis is true. Small p-values tell you that the hypothesis is probably wrong, which is what you wanted to show anyway.

There is big money in small p-values. Its what you need to ‘show’ that a particular treatment for a particular ailment works in order to bring your pills to the market. [Insert cheap joke about big pharma and certain dysfunctions here.]

Now whats a small p-value?

Well, Ronald Aylmer Fisher wrote the following in The Journal of the Ministry of Agriculture, in the year of the Lord 1926:

If one in twenty does not seem high enough odds, we may, if we prefer it, draw the line at one in fifty (the 2 per cent. point), or one in a hundred (the 1 per cent. point). Personally, the writer prefers to set a low standard of significance at the 5 per cent point, and ignore entirely all results which fail to reach this level. A scientific fact should be regarded as experimentally established only if a properly designed experiment rarely fails to give this level of significance.

In other words, Fisher pulled the number 1/20 = 0.05 out of his ass thin air and was honest about it. Since then, people have followed Fisher’s words as reported in the reputable Journal of the Ministry of Agriculture. Not with pulling numbers out of various orifices, but with sticking to p=0.05 as the special value that shows ‘significance’, like a religious sermon.

Now lets have a look at p-values reported in various recent papers. Say, 3627 of them. This is where the histogram comes from [1]. (The original paper [2] is behind a pay wall. Thank you, Taylor & Francis.)

Look, too many p-values less than 0.05!  And too few above 0.05!  How peculiar, and utterly surprising!

Some possible explanations [1]:

Publication bias. Report a p-value just above 0.05? Referees will shoot you down.

Give up. Found a p-value just above 0.05? Don’t bother writing up.  Because see above.

Tweaking. Fiddle around with your analysis until you make it below 0.05.

Dynamic sample size. Fiddle with the sample size until you make it below 0.05.

Slice and dice. Only report p-values for ‘appropriate’ subsets of data.

Outliers. Only report outliers.

One item is missing from this list: Fraud.

Caveat: the 3627 reported p-values all come from psychology journals. Be careful before you start laughing and point fingers at that particular discipline. Are you sure this stuff doesn’t happen in your neck of the woods?

[1] http://www.graphpad.com/www/data-analysis-resource-center/blog/a-peculiar-prevalence-of-p-values-just-below-051/

[2] http://www.ncbi.nlm.nih.gov/pubmed/22853650

Channeling chi: blocking channel for pain

Following up on Buddhini Samarasinghe’s knockout mouse post (http://goo.gl/DjWewM) which you should read but I know most of you read it already, here’s a mouse that will knockout scorpions and centipedes. The grasshopper mouse (Onychomys torridus) is an awesome fighter. Besides howling at the moon, they can block the pain from some types of venom.

Nociceptors are sensory neurons that are associated with pain. They used to be called pain receptors but we know now that they are involved with sensing more than just pain. Some venoms bind to the sodium channel in nociceptors, causing intense pain (among other things).

The unique thing about the grasshopper mouse is that it has a mutation that actually uses the venom to block pain, i.e. block the transmission of the signal from the nociceptor to the brain. Now that’s pretty cool.

Grasshopper mouse vs. centipede.

http://goo.gl/VCMDaO via National Geographic 

Grasshopper mouse howling

http://goo.gl/b6blp via WIRED 

Zoologger: Mouse eats scorpions and howls at the moon

http://goo.gl/CDqZmV via New Scientist 

Image source: http://goo.gl/YQfR9Z

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Hero shrew (Scutisorex somereni): put your back into it

I stumbled onto this amazing story browsing through the BlinkFeed on my HTC One via The Verge http://goo.gl/MQEo8h

Imagine something weighing thousands of times your weight, standing on you? The hero shrew can handle that. I usually don’t like to quote articles in their entirety. However, this is way out of my area and I like the version from The Field Museum news feed.

Over a century ago, explorers in the Democratic Republic of Congo noted a strangely large and hairy shrew – that’s right, a shrew. When they commented on the shrew to the locals, they were told, “We wear this animal as a talisman around our necks, so that we will be invincible.” The explorers, confused as to how such an animal could be thought to make a person invincible, watched in amazement as a full-grown man stood on the back of the shrew for over five minutes, and the animal walked away, unharmed!

Thus, the shrew came to be called the Hero Shrew. Just this week, Field Museum scientists and international collaborators identified a new species of Hero Shrew – the mammal with the most bizarre backbone on Earth.

Its name? Thor’s Hero Shrew.

The remarkable spine of the Hero Shrew is unique among mammals, in that the lower vertebrae are both wider and longer, than those of other mammals. This gives the animal extraordinary strength! In fact, the unique vertebrae of the Hero Shrew make the spine up to four times more robust than other mammals. It’s no wonder the authors gave it a name that invokes Thor, the god of strength in Norse mythology!

Until now, there have been no other species of the Hero Shrew, and the spine has been an enigma to scientists, because it provides no known advantage to the animal. Now, however, scientists suggest that these shrews may position themselves between the trunk and leaf bases of Palms, and use their unique spine to pry the leaf base away from the trunk and gain access to grubs that are otherwise hidden from predators.

The specimen now residing at The Field Museum is a holotype (meaning the single physical example of this particular species that was originally used in its identification), so scientists around the world will use this very shrew as the golden standard for any future research done on this species.

Second image and text from: http://goo.gl/CYyDWN

Here’s the link to the article and the source for the first image.

A new hero emerges: another exceptional mammalian spine and its potential adaptive significance.

Stanley WT, Robbins LW, Malekani JM, Mbalitini SG, Migurimu DA, Mukinzi JC, Hulselmans J, Prévot V, Verheyen E, Hutterer R, Doty JB, Monroe BP, Nakazawa YJ, Braden Z, Carroll D, Kerbis Peterhans JC, Bates JM, Esselstyn JA.

Biol Lett. 2013 Jul 24;9(5):20130486. doi: 10.1098/rsbl.2013.0486. Print 2013.

http://www.ncbi.nlm.nih.gov/pubmed/23883579

The third image is an example of a hole left behind from a Rhinoceros beetle larvae in a palm tree http://goo.gl/sSYPYy

Based on the hypothesis, the hero shrew would wedge itself on the opposite side of where that hole is (of course the hole wouldn’t be there as the shrew would want it when it’s still a larva).

The final photo is from National Geographic 

http://goo.gl/4PpNoJ

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Orange you glad to see science?

Thanks Fadia Lekouaghet for sharing this post and introducing me to Caleb Charland’s art. In grade school, kids are shown how to make a circuit with a lemon or tomato but this is better way to get the point across and get kids interesting in science.

Here’s a link for those that want to try at home.

http://www.ehow.com/how_4884677_make-light-bulb-experiment.html

See the explanation of how it works in the comment by Fernando J. Rodriguez 

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Originally shared by Fadia Lekouaghet

What if pictures begin as simple questions…

Caleb Charland is a photographer that captures the everyday physical phenomena which we never think about in a unique and inspiring way.

The photo below is one of his works. it shows an *Orange Battery*.

The photographer uses still-life arrangements, for instance, apples and potatoes as an electrical source for the lamp that illuminates the resulting photograph. In this image he used the orange’s natural wedges as the cells for the battery, which were held up-right with an armature of small wooden skewers.

The amazing work took 14 hours of exposure.

Caleb Charland work: http://goo.gl/qP6xcp

The realm of magic

Thanks Kee Hinckley for posting this. I’m often debating with various conspiracy theorists on G+. Whether it’s big pharma conspiracies or Monsanto/anti-GMO conspiracies, this video helps put the anti-science proponents in perspective. When people use big pharma as an argument against a lot of the biomedical science that I post about, it does two things. First it insults people like me that spend their careers using science to fight things like cancer. When conspiracy theorist say things like “big pharma has a cure for cancer but it’s more profitable to keep the cure secret”, it implies that I, along with my colleagues, are bumbling idiots or unscrupulous scum. Well I’ve said many times, big pharma must have the wrong address for me because I drive a VW. I wish I knew who is cashing my checks from big pharma.

Secondly, the conspiracy theory card is a cop-out. It’s very difficult to argue against because the conspiracy theorists just negates everything you say because you are part of the conspiracy. It’s very convenient and lazy.

My favorite quote from the video is:

Once you’re forced to hypothesize whole new technologies to keep our conspiracy possible, you’ve stepped over into the realm of magic. It demands a deep and abiding faith in things you can never know.

and knowing vs. believing is very powerful.

Kee Hinckley posted the mobile link, which is why I didn’t reshare his post. However his comments are also worth sharing.

This video has a very important lesson for people who believe every government conspiracy theory out there.

You don’t have to watch the whole thing, although he does an excellent job of showing how the technology available in 1969 was incapable of faking a moon landing. But watch the last two minutes (11m and on). There he explains why it matters that you don’t fall for conspiracy hoaxes. Because yes, the government does lie, and that makes it even more important that you have the critical skills to distinguish the real problems from the made up ones. When your conspiracy theory starts relying on faith (whether in technology, ridiculous numbers of secret organizations, or anything else) you’ve crossed the line.

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http://www.youtube.com/watch?v=sGXTF6bs1IU

When in Rome, build something concrete

Researchers at UC Berkeley are studying ancient Roman concrete in an effort to come up with a durable, yet green concrete. Shipping was instrumental to the expansion and sustainability of the Roman Empire. Using volcanic ash and seawater, the Romans developed concrete that has withstood the harsh marine environment for over 2,000 years. Scientist used the Advanced Light Source at Lawrence Berkeley National Laboratory (Berkeley Lab) to look at fine structures in the Roman concrete for the first time.

Roman concrete has a smaller carbon footprint because the modern cement (Portland cement) burns calcium carbonate (limestone) and clays at 1,450 deg C while lime used in Roman concrete requires only two thirds of that.

If Roman concrete is so good, why is it not still used? As the Roman Empire declined, the need for shipping and therefore the need marine concrete diminished. Also, modern concrete takes a fraction of the time to cure, compared to Roman concrete.

Edit

I should have defined what concrete is. Concrete is a composite material, made of “filler” (e.g. pebbles) and a binder (cement). So what is cement? More importantly, what is Portland cement, which is mentioned in the article and is the most common type of cement used. Portland cement is calcium silicates mixed with aluminum and iron containing clinker phases. (http://en.wikipedia.org/wiki/Portland_cement). So what are clinker phases? Clinkers are balls of sintered (baked) material made by taking a mixture of materials and heating them with very high heat. So the big difference between Roman concrete and modern concrete is really the clinker, not so much the filler. Also note that Roman concrete does not use steel reinforcing bars (rebar), so modern concrete has much higher tensile strength.

Cement Clinker on the Belt

More here:

http://newscenter.lbl.gov/news-releases/2013/06/04/roman-concrete/

Image source and reference: http://newscenter.berkeley.edu/2013/06/04/roman-concrete/

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