Animated Book Review of Bad Science by Ben Goldacre

Ben Goldacre is one of my current favorite authors. In Bad Science, he looks at flaws within industries and different entities: supplements, pharma, research, ‘alternative’ and ‘natural’ non-sense, and so on. So, he doesn’t take sides. In fact, I’d better say his argument is in favor of developing good thinking skills to be able to spot deception; skills in stats, maths, and psychology to name a few. I think it’s in each other’s power to become knowledgeable of human irrationality.

Should you decide to self-educate, you may be more prepared in avoiding being deceived. It’s not that all these entities should seek your betterment; afterall, most of them are for-profit, so it’s in their best interest to maximize their financial gains, even if it has to do with exploiting your gullibility. Anyway, more soft-rant in the video:

Genetic Mutations and Diabetes – My Analysis of 115 Genomes

genetic-mutations-and-diabetes-my-analysis-of-115-genomes

Last week I began analyzing genotype and phenotype data available through OpenSNP, a platform where people share this type of information.

The first phenotype I looked into was about smoking.

Using Python I took the smoker status reported by users and correlated it with a mutation (rs1051730) in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. A few genome wide association studies (GWAS) linked this mutation to nicotine dependence, alcohol abuse, and susceptibility of developing lung cancer.

My point with the post was to offer a proof of concept and to reveal/interpret the data I got out of my Python analysis. I wanted to create a precedent so that others could freely use and improve my scripts and my approach.

Of course, if you’re a user of OpenSNP, you can gain a lot of insight by looking at your own genotype for this SNP (single nucleotide polymorphism) and correlate it with my findings. To see the exact details of what I did and to download the Python codes, go and read the post.

Anyhow, I decided to continue with another analysis.

Analysis of 243 Genomes – My First Report [Nov. 2016]

analysis-of-243-genomes-my-first-report-nov-2016-1

About two weeks ago I learned about this website OpenSNP where people can share their genetic information and not only. It is similar to 1000genomes, but I think it is much more interesting to work with because aside of genetic information (SNP sequencing, exome, etc.) most users also share phenotype data; data is not anonymized. This is what sparked my interest.

With phenotype data and user’s genetic mutations – SNPs – (or other relevant genetic information), I could run analyses and find possible correlations. This is applied big data.

In this post, I’ll explain how I conducted my first analysis. I want to provide an outline with enough relevant details so I can have a reference point to make things easier in future analyses. Of course, I could simply do this in private but I’d rather post it on the blog so that others who are interested to run similar analyses can have starting point.

This involves: knowledge of genomics, genomics related software and raw data formats, programming, and a lot of patience.

My Encounter with Curiosity, the Mars Rover

As I came out of the number 1 subway station in Lower Manhattan on Wednesday evening I encountered a scene that was different to what I was used to.

i-met-curiosity-the-mars-rover-1

Instinct had me enter, but I couldn’t stay long because I was already late for an evening lecture at the genome center right across the street. So I rushed asking for details and deciding I was going to come back another day.

Radiotolerance Lessons from the Tardigrades

radiotolerance-lessons-from-the-tardigrades

Image: female tardigrade containing eggs.

Hashimoto and colleagues (2016) published an article in Nature recently:

Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

Tardigrades, a.k.a. water bears, are some of the most extreme organisms, capable of surviving in the most un-habitable environments and being exposed to insults that would kill other living beings. Examples include: very high and very low temperatures, high doses of radiation, high pressure, outer space, and others.

Here are some of the particularities (in terms of gene expression) of tardigrades:

What I’ve Been Reading Recently – My Bookshelf #10

Reading a book at the beach

Intro

I read more than 70 books this year (as of August 2016). I don’t speed read. I allocate sufficient time every day to ‘parse’ books. I mostly read non-fiction. Some of the books are in audio format. Obviously I do not listen to textbooks and programming books. I choose the audio format for the non-technical and more practical ones.

My current interests: genomics, bioinformatics, machine learning, and human irrationality.

Additionally, for knowledge acquisition, I also:

– read research studies
– listen to interviews
– watch lectures and seminars
– take online courses

You can find all past book/reading related posts: #1 #2 #3 #4 #5 #6 #7 #8 and #9

Current philosophy:

The more I read, the more I realize the little I know.
Reading is not a hobby; it is part of my daily routine.
I avoid being superficial. I don’t want to skim through the books I read.
I read 7-10 books at a time.
I think that with practice I’ve been able to develop the skill of reading faster (!=speed reading).

10-Lecture Course on Science Based Medicine – And Alternative Practices

10-Lecture Course on Science Based Medicine - And Alternative Practices

Introduction

I started watching these lectures on Youtube about two months ago, a bit every day, slowing digesting the information and doing additional searches on the web whenever I found that a topic sparked my interest.

These lectures are presented by Dr. Harriet Hall, a retired family physician and Air Force Colonel. According to Skeptic:

“She writes about alternative medicine, pseudoscience, quackery, and critical thinking. She is a contributing editor to both Skeptic and Skeptical Inquirer, an advisor to the Quackwatch website, and an editor of Sciencebasedmedicine.org, where she writes an article every Tuesday.”

You can find more about Dr. Hall at SkepDoc.info.

I appreciate the work Dr. Hall and others are doing in informing the public about the perils of quackery. And from what I perceive from her work, she doesn’t only try to bring awareness about bad science in alternative and non-scientific practices, but also in conventional medicine.

Thus, I consider her a good example of impartiality. She takes on conventional medicine and its numerous inconsistencies in lecture 9. No matter the pitfalls of conventional medicine, I’d say that it’s better regulated and more science based (given that you can filter through poorly conducted studies – see lecture 9) than bogus medical practices and claims.

I recommend this course to people who want to become more educated in critical thinking and to those who want be less prone to being phished for phools. Here are the titles of the lectures and a few notes on each.

Baloney Detection – How to Distinguish between Science and Pseudoscience [A Short Guide]

Baloney Detection - How to Distinguish between Science and Pseudoscience [A Short Guide]

Introduction

“When we’re growing up (!and, often in adult life) we tend to be pretty credulous. We just believe almost anything that people tell us, especially if it comes from authorities, experts, textbooks, politicians, television, Youtube, and the Internet. I mean, there’s just this sort of sea of information coming at us. And how can you tell the difference between: it’s right or wrong? How do you know?!” Michael Shermer (emphasis mine)

There’s way too much misinformation ‘out there’. And some of it is on purpose – disinformation. Whether it happens on the Internet or within your circle of friends, family and acquaintances, you (and I) are being bombarded with non-sense ad nauseam.

Filtering through, to get some valuable information, whenever that’s possible, is not easy. For this purpose, Carl Sagan and Michael Shermer formulated what they call: a baloney detection kit.

It started with an essay written by Sagan a long while ago [2]. In it, Sagan advises people on how to avoid logical and rhetorical fallacies. Acknowledging the value of this manifesto, Michael Shermer devised a more accessible and easily readable format of Sagan’s words [1].

Pure, raw information is of immense value today. Most information that reaches your senses is coated with personal filters and prejudices; it is distorted, manipulated, or modified in one way or another.

Here, I want to reignite awareness on Sagan and Shermer’s advice, hoping that it will help us better filter through this mountain of non-sense and also help us stave off the bad influence of malicious parties.

Rare Things happen all the Time – Another Example of Deception

Rare Things happen all the Time - Another Example of Deception

Introduction

Far from the intent of teaching deception, I’m writing this to bring awareness to some of the practices of dubious entities towards the gullible masses. Most of what you’re going to read is not my original thought. It is from a recent book that I read. I will do my best to add some personal interpretation whenever I find it appropriate.

The Priming Effect – Your Thoughts, Friends, Environment = Future You

The Priming Effect - Your Thoughts, Friends, Environment = Future You - 2

Introduction

With my head stuck into Thinking Fast and Slow, the voluminous book by Nobel Laureate Daniel Kahneman, I started becoming more familiar with the field of behavioral economics. Kahneman discusses extensively about cognitive biases and automatic (unconscious) mechanisms that drive human behavior (unconscious to you and me of course – unless you are actively aware of them).

Such mechanisms may allow deceitful/scheming/manipulating entities to exploit us for different purposes.

Other biases may provide rationale behind personal development babble. One of them, the focus of this write-up, is the priming effect. It caught my interest and it made me read a few scientific papers about it. Over the last few decades the priming effect has received a cocktail of appraisal and criticism on behalf of the research community.

In short, “priming is an implicit memory effect in which exposure to one stimulus (i.e., perceptual pattern) influences the response to another stimulus.” (more)

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