Dr. Larry Dossey, author of The Power of Premonitions, has the audacity to educate us about the scientific method, appropriately enough in perhaps the most prominent anti-scientific venue on the web, the Huffington Post. He starts off with a horrid straw man quoted from Jeremy Rifkin:

The scientific observer is never a participant in the reality he or she observes, but only a voyeur. As for the world he or she observes, it is a cold, uncaring place, devoid of awe, compassion or sense of purpose. Even life itself is made lifeless to better dissect its component parts. We are left with a purely material world, which is quantifiable but without quality … The scientific method is at odds with virtually everything we know about our own nature and the nature of the world. It denies the relational aspect of reality, prohibits participation and makes no room for empathic imagination. Students in effect are asked to become aliens in the world.

This is a Hollywood level cardboard stereotype. It certainly does not resemble what I have experienced as science or scientists. Without getting too much into this side point, Rifkin himself is a controversial figure in the scientific world. He is an economist, not a scientist, and just to give you a flavor of his reputation, Stephen J. Gould once wrote about his work that it was, “a cleverly constructed tract of anti-intellectual propaganda masquerading as scholarship.”

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Or – Why are there so many engineers on the list of scientists who doubt Darwin?

At a recent live SGU show (at Dragon*Con 2009) a questioner asked why it was that so many of the scientists who have added their name to the list of those who doubt Darwin were – and then I cut him off and finished for him – engineers. He was not the first person to make this observation. (You can download the list here: http://www.dissentfromdarwin.org/download.php)

First, on a separate note, this list has been the focus of much ridicule because after years of scouring the globe they have only managed to come up with 700 scientists willing to sign the list. And, whenever they add scientists to the list they boast that the number of scientists dissenting from Darwin is growing, as if the percentage of scientists is growing, and therefore the scientific community is moving away from evolutionary theory (which they tellingly equate with Darwin). No – they just added another buffoon to their list.

Also, I have to point out that the National Center for Science Education, to parody the silliness of this list, launched Project Steve, and have now listed 1,107 scientists named Steve (or some variation of Steve) who support evolution (and of which I am a proud member).

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Genetic engineering is a rapidly progressing scientific discipline, with tremendous current application and future potential. It’s a bit dizzying for a science communicator who is not directly involved in genetics research to keep up. I do have some graduate level training in genetics so at least I understand the language enough to try to translate the latest research for a general audience.

Many readers have by now heard of CRISPR – a powerful method of altering or silencing genes that brings down the cost and complexity so that almost any genetics lab can use this technique. CRISPR is actually just the latest of several powerful gene-altering techniques, such as TALEN. CRISPR is essentially a way to target a specific sequence of the DNA, and then deliver a package which does something, like splice the DNA. But you also need to target the correct cells. In a petri dish, this is simple. But in living organism, this is a huge challenge. We have developed several viral vectors that can be targeted to specific cell types in order to deliver the CRIPR (or TALEN), which then targets the specific DNA.

Now I would like to present a different technique I have not previously written about here – alternative splicing. A recent study presents what seems like a significant advance in this technology, so it’s a good time to review it. “Alternative splicing” refers to a natural phenomenon of genetics. Genes are composed of introns and exons. I always thought the nomenclature was counterintuitive, but the exons are actually the part of the gene that gets expressed into a protein. The introns are the part that is not expressed, so they are cut out of the gene when it is being converted into mRNA, and the exons are stitched together to form the sequence that is translated into a protein. Alternative splicing refers to the fact that the way in which the introns are removed and the exons stitched together can vary, creating alternative forms of the resulting protein. This dramatically increases the number of different proteins that an organism’s genes can code for, because each gene can potentially code for multiple protein variants through alternative splicing.

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This is a great idea, and in fact is long overdue. The NIH is awarding various grants to establish educational materials and centers to teach principles of scientific rigor to researchers. This may seem redundant, but it absolutely isn’t.

At present principles of research are taught in basic form during scientific courses, but advanced principles are largely left to individual mentorship. This creates a great deal of variability in how well researchers really understand the principles of scientific rigor. As a result, a lot of research falls short of scientific ideals. This creates a great deal of waste in the system. NIH, as a funding institution, has a great deal of incentive to reduce this waste.

The primary mechanism will be to create teaching modules that then can be made freely available to educational and research institutions. These modules would cover:

biases in research; logical fallacies around causality; how to develop hypotheses; designing literature searches; identifying experimental variables; and reducing confounding variables in research.

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There is plenty of fraud and corruption in the world, even in the halls of science. No one has a monopoly. But there are some hot spots that deserve specific attention. Recently significant concerns have been raised about the published research of Xuetao Cao, a Chinese Immunologist. This story is newsworthy because Cao is not just any immunologist – he is also the President of Nankai University, in Tianjin, China. But more to the point – he is the Chairman of research integrity in all Chinese research. When your head of research integrity is exposed for massive scientific fraud, you have a problem.

Here is a thorough treatment of the evidence for fraud, which covers over 50 published papers. The fabrication of data was noticed because much of it has to do with pictures, of either western blots, gels, flow cytometry images, and microscopy images. There appears to be two general types of fabrication going on. One type results from sending the same sample multiple times through analysis, but treating the data as if it came from different samples. In this case the resulting imaging will be strikingly similar in pattern, but not identical. The second type of fabrication is to simply photoshop copy and paste images.

Either way, the resulting data fabrication is undeniable once it is noticed. The images are simply too similar (and again, sometimes identical) to be genuine data. Once researchers started pouring through Cao’s other papers, the extensive fraud became obvious. When confronted with this revelation online, Cao responded by first standing behind his work, then stating:

Nevertheless, there is no excuse for any lapse in supervision or laboratory leadership and the concerns you raised serve as a fresh reminder to me just how important my role and responsibility are as mentor, supervisor, and lab leader; and how I might have fallen short.

Wow – you see what he just did there? He simultaneously apologized and took responsibility, but only for failure of supervision. So essentially he is throwing all of the people who work for him under the bus. Either way, however, this is really bad for Cao. Even in the best case scenario, all the fraud was perpetrated by others under his watch. Keep in mind, he is in charge of research integrity for all of China, but apparently can’t keep an eye on his own lab. There are certainly famous cases where research assistants were the ones perpetrating the fraud. Another immunologist, Jacques Benveniste, claimed to have evidence of immunological activity from high “homeopathic” dilutions. An investigation found his results to be highly unreliable at least, and likely straight-up fraudulent (although may have been do to really sloppy techniques and bias). But it also appears that the positive results all seemed to come from one lab assistant, Elizabeth Davenas – certainly a disturbing pattern.

Perhaps a similar pattern will emerge from Cao’s lab, but it seems unlikely that an overzealous assistant can be responsible for data fabrication in 50 published studies. This is clearly a systemic problem.

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Continued from Part I

5) How to Analyze a Scientific Study

I don’t expect a non-scientist, or even a scientist far outside their area of expertise, to be able to do a detailed analysis of the strengths and weaknesses of a study. That is what peer-review is for. However, there are some basic rules of thumb that could give even a lay person a rough idea how seriously they should take a study. Always ask at least the following questions:

Is the study controlled in some way? Was the treatment group compared to a control group, or was the alleged effect compared to some baseline?

Is the study blinded? Were the primary measurements or assessments performed by someone who was blinded to whether or not the alleged effect is supposed to be present?

Are the outcomes being measured subjective or objective? How are they being measured? What do they really mean?

How large is the study? Studies with small numbers of subjects or measurements (less than 50 per group is a good rule of thumb) are considered small and unreliable.

Is the study an observation or an experiment? Are they just looking for some correlation  (in which it is difficult to make statements about cause and effect), or are they controlling for variables and isolating the one factor of interest?

What is the reaction of the scientific community to the study? Are experts generally critical or excited about the results? Continue Reading »

What does it mean to be scientifically literate? There is no completely objective answer to this question, it can be defined in multiple ways and the bar can be set anywhere along a spectrum.

Many tests of scientific literacy essentially ask a series of scientific facts – they are tests of factual knowledge, but not scientific thinking. This glaring deficit has been pointed out many times before, and was so again in a recent editorial by Danielle Teller. She writes:

There are a number of problems with teaching science as a collection of facts. First, facts change. Before oxygen was discovered, the theoretical existence of phlogiston made sense. For a brief, heady moment in 1989, it looked like cold fusion (paywall) was going to change the world.

I agree. A true measure of scientific literacy should be a combination of facts, concepts, and process. Facts are still important. Concepts without facts are hollow, and facts without concepts are meaningless. Both need to be understood in the context of the process that led us to our current conclusions.

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Conflict and crisis, while uncomfortable and even painful, can be a good thing if responded to constructively. The skeptical movement is having a bit of an identity crisis, which is an excellent opportunity to closely examine what and who we are, our goals, and our differences.

This post is a continuation of my prior two recent posts on this topic. Each post led to hundreds of comments and a very active discussion of all of the issues. To spare those who are interested from having to wade through hundreds of comments, I will try to summarize where I think we are with the discussion. I do think it has resulted in a better understanding on my part of the relevant issues and opinions.

The heart of the controversy is over the scope of activist skepticism. What topics should we address, how is “skepticism” defined, and what approach should we use. The main problem is that there are as many answers to this question as there are activist skeptics. Our movement, such as it is, has mostly been a bottom-up grassroots type movement, with individuals and organizations spreading all over the map in terms of every important aspect of the identity question. This has led many to compare “organized skepticism” to herding cats.

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Facilitated Communication (FC) is a technique for allegedly aiding those with communication impairment, such as some people with autism, to communicate through typing or pointing at a letter board. The idea is that some children have greater cognitive ability than is apparent through their verbal skills, but they lack the motor skills to type or write. The facilitator in FC is trained to hold and support their client’s hand, to help stabilize it, so that they can type out their thoughts.

FC was enthusiastically embraced by the special education community in the late 1980s and early 1990s but problems quickly emerged, namely the question of authorship – who is doing the communicating, the client or the facilitator?

The scientific evidence came down clearly on one side of that debate – it is the facilitator who is the author of the communication, not the client. The American Psychological Association has reviewed the available evidence and produced a position statement that concludes:

The short version of this long story is that study after study showed that facilitated communication didn’t really work. Apparently, the positive results that had generated so much enthusiasm were the results of a subtle process in which well-intended facilitators were answering questions themselves – without any awareness that they were doing so.

A 2001 review by Mostert came to the same conclusion – that the evidence supports the conclusion that the facilitators are the authors of communication in FC. He also points out that there is a relationship between the rigor of the studies and the results. The most rigorously blinded studies are all negative, studies with some blinding but also with problems are mixed and often show some positive results, and unblinded studies are all positive, showing dramatic effects. This pattern mirrors that of ESP and many other pseudosciences that are primarily the result of self deception.

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If ever there were an oxymoron it is this phrase: “scientific heresy.” I understand it may be used at times as a bit of poetic license,  a metaphor for a new and seemingly outrageous (but scientific) idea, but I despise it none-the-less. The phrase is more often used as a direct or implied criticism of science and scientists, and generates deliberate confusion.

The notion of heresy is – well, Wikipedia actually has a good summary:

Heresy is a controversial or novel change to a system of beliefs, especially a religion, that conflicts with established dogma. It is distinct from apostasy, which is the formal denunciation of one’s religion, principles or cause, and blasphemy, which is irreverence toward religion. The founder or leader of a heretical movement is called a heresiarch, while individuals who espouse heresy or commit heresy, are known as heretics.

Heresiology is the study of heresy.

Now, I’m no heresiologist, but it seems to me that the core of the notion of “heresy” is inexorably tied to the notion of dogma – a fixed set of beliefs promoted and sustained through authority. Dogma and heresy are anathema to science.

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