Still anti-medicine?

Still anti-medicine?

There are some people that comment that modern medicine is bad. Certainly it isn’t perfect; nothing is. To say that it is all bad is silly, in my opinion. For the anti-vaxxers, there’s a whole list of diseases that we’ve eradicated due to vaccinations. The NPR piece linked helps drive home the point.

A change came when, in 1995, the first triple-drug combinations became available, Lennox says. He saw an amazing transformation take place, where people who were on their deathbed were discharged within a month.

“It was the most amazing thing and it still is,” he says. “We still get people who come in at the end stages of AIDS and if we catch them in time, many of them are restored to normal health.” [Dr. Jeffrey Lennox]

#ScienceEveryday  when it isn’t #ScienceSunday  

#Anti_anti_intellectualism

http://www.npr.org/2012/07/22/157199216/testing-treatment-key-weapons-in-aids-fight

the idea of the contradiction comes from what I see as the deepest misunderstanding about science, which is the idea…

the idea of the contradiction comes from what I see as the deepest misunderstanding about science, which is the idea that science is about certainty.

Because obviously it’s easy to suggest that the earth sort of floats in nothing, but then you have to answer the question: why doesn’t it fall? The genius of Anaximander was to answer this question. We know his answer, from Aristotle, from other people. He doesn’t answer this question, in fact. He questions this question. He says why should it fall? Things fall toward the earth. Why the earth itself should fall? In other words, he realizes that the obvious generalization from every small heavy object falling, to the earth itself falling, might be wrong. He proposes an alternative, which is that objects fall towards the earth, which means that the direction of falling changes around the earth. […]

…what is being challenged at every step is not the theory, it’s the conceptual structure used in constructing theories and interpreting the data. In other words, it’s not changing theories that we go ahead, but changing the way we think about the world. […]

Science is not about certainty. Science is about finding the most reliable way of thinking, at the present level of knowledge. Science is extremely reliable; it’s not certain. In fact, not only it’s not certain, but it’s the lack of certainty that grounds it. Scientific ideas are credible not because they are sure, but because they are the ones that have survived all the possible past critiques, and they are the most credible because they were put on the table for everybody’s criticism. […]

Like João Figueiredo I was tempted to keep quoting the article. It’s simply a fantastic read. I come across some of the ideas/comments presented in the article when anti-science people comment on my posts or friend’s posts. At first glance, the anti-science people might find support in this article. However, if you read the whole thing, what he says at the end resonates with me and hopefully with other pro-science advocates.

#ScienceEveryday   curated by ScienceSunday (Allison Sekuler Rajini Rao Robby Bowles and me)

Originally shared by João Figueiredo

Magnificent interview with quantum physicist Carlo Rovelli, where he dwells on what is Science and his passion with the pre-Socratic philosopher Anaximander:  

Let me tell you a story to explain what I mean. The story is an old story about my latest, greatest passion outside theoretical physics: an ancient scientist, or so I would say, even if often he is called a philosopher: Anaximander. […]

Until him, all the civilizations of the planet, everybody around the world, thought that the structure of the world was: the sky over our heads and the earth under our feet. There’s an up and a down, heavy things fall from the up to the down, and that’s reality. Reality is oriented up and down, heaven’s up and earth is down. Then comes Anaximander and says: no, is something else. ‘The earth is a finite body that floats in space, without falling, and the sky is not just over our head; it is all around.’ […]

How he gets it? Well obviously he looks at the sky, you see things going around, the stars, the heavens, the moon, the planets, everything moves around and keeps turning around us. […] nobody else got to this simple realization that the sky is not just over our head, it’s also under our feet. Why?

Because obviously it’s easy to suggest that the earth sort of floats in nothing, but then you have to answer the question: why doesn’t it fall? The genius of Anaximander was to answer this question…_

How? Well, you can either watch the interview or read the transcript… If you need some context on Anaximander, I suggest The History of Philosophy Without Any Gaps podcast on him:

http://www.historyofphilosophy.net/anaximander-anaximines 

via http://scipsy.tumblr.com/

http://edge.org/conversation/a-philosophy-of-physics

FDA and medical smartphone apps

FDA and medical smartphone apps

From the article:

…federal regulators lurched into action a year ago, offering their thinking on how to police this vast new frontier. Just as they were putting the finishing touches on a plan, lawmakers intervened. The Senate moved to put the plan on hold after tech firms convinced lawmakers that more government oversight would stifle innovation and cost jobs.

“There are two completely different mindsets,” said Merrill Matthews, a resident scholar at the Institute for Policy Innovation. “The app people think: Where is there a need and how do I fill it? And the FDA thinks: Where is there a problem and how can I control it?”

There’s a fine balance between a regulation free, wild wild west scenario and the stupidity which is our patent, trademark, and copyright system. It’s true that the mobile tech space moves way too fast for an agency like the FDA. However, I guarantee, the first person that gets hurt from a medical app is going to sue everyone under the sun and blame the government for not protecting the average Joe/Jane.

#ScienceEveryday  

http://www.chicagotribune.com/business/ct-biz-0626-health-apps-20120626,0,4426493.story

Blue for you or Pretty in Pink?

Blue for you or Pretty in Pink?

About  week ago I posted some pictures of my Hydrangeas that were just starting to bloom. http://goo.gl/Gn47h  I noticed that on the same plant, some of the flowers were blue and others were pink. I knew that pH played a role but I found out that it is actually the aluminum in the soil that make the blue pigment possible. So for ScienceSunday curated by Allison Sekuler Rajini Rao Robby Bowles and me, I had to dig up more info to post along with pictures from today.

When the pH is acidic, aluminum in the soil, mostly from clay, allows a metal complex of aluminum and a anthocyanin, named delphinidin 3-monoglucoside, to form. After the pictures, the first figure is of the aluminum complex. The next figure shows various blue flowers with sections cut revealing the pigment cells and protoplasts.

Although the next two figures are about Morning glories, they were too interesting to pass up. A certain ScienceSunday co-curator always has her eyes on certain channels. Similar to the previous figure, there is a cross section-cut revealing the pigmented cells. However, the paper and figure go on to discuss how the Morning glory does not have metal complexation. The petal color changes during flower opening due to pH changes which were measured in the second part of the figure. The final figure show the purported ion channel mechanism.

Plants can be beautiful. When you throw in a dash of science, they can be beautiful and intriguing.

Edit I forgot to add that a lot of insects leave hydrangeas alone. Why? Aluminum toxicity – win – win for us gardeners.

Sources: 

Kumi Yoshida ,  Mihoko Mori and Tadao Kondo

Nat. Prod. Rep., 2009,26, 884-915

DOI: 10.1039/B800165K http://goo.gl/VGlZH

http://goo.gl/CcFg6

So is it Men At Work – Blue For You (1983) or The Psychedelic Furs – Pretty In Pink ?

#ScienceSunday #ScienceEveryday

What’s buggin’ you?

What’s buggin’ you?

On NPR they discussed the first catalog of bacteria, viruses, and other microorganisms that are in and on our bodies. I read somewhere that the microbes on are body along with our diet help make our smell unique, at least that’s what helps dogs identify us by. I need to find a link for that. This part blew me away:

Scientists have already discovered some intriguing clues. For example, the microbes in a pregnant woman’s birth canal start to change just before she gives birth. Scientists think that’s so their babies are born with just the right microbiome they’ll need to live long, healthy lives.

#ScienceEveryday

http://www.npr.org/blogs/health/2012/06/13/154913334/finally-a-map-of-all-the-microbes-on-your-body

Scanning – Tumors and G+

Scanning – Tumors and G+

So I’m at work catching up on scanning some slides of human squamous cell carcinoma tumors, SCC61. Actually they are xeongrafts in mice legs. The hematoxylin and eosin stains (http://goo.gl/Sq9Eq) make it easy to identify cancer (the purple part, the pink part is muscle). While I’m scanning each slide, I was also catching up on G+. I click on a post from Buddhini Samarasinghe that she warns is long but worth the read (http://goo.gl/tiZtc). It’s an interview with Dr. Otis Brawley about his book, “How We Do Harm: A Doctor Breaks Ranks About Being Sick in America”.

He works at Grady hospital in Atlanta, is currently chief medical officer at the American Cancer Society, and graduated from the University of Chicago. Grady sounds like Cook County hospital in Chicago (think ER TV show, now called Stroger), you wouldn’t want to go there but a lot of cops do because they are very experienced in GSW-trauma. Chicago is still the #1 segregated city (http://goo.gl/Vyio8). …the abstract, scholarly term “health disparities” acquires a very real smell of a rotting breast.

Here is the problem: Poor Americans consume too little healthcare, especially preventive healthcare. Other Americans-often rich Americans-consume too much healthcare, often unwisely, and sometimes to their detriment. The American healthcare system combines famine with gluttony.

I don’t want to quote the whole article but I ♥ the Wayne Gretzky quote, “You miss every shot you don’t take”.

There’s so much of the article that resonated with me. I do cancer research. I work in an urban hospital where I see firsthand, the disparities he speaks of. I know breast cancer survivors and our group does breast cancer research. Previous post on breast MRI. http://goo.gl/VSrU4 He’s taken heat about PSA testing but it is something we talk about at work quite often and agree with him.

Anyway, enough babbling. Read the post from Buddhini Samarasinghe

#ScienceEveryday #CancerResearch

Alarming science discovery…

Alarming science discovery…

Here’s a news article, In cancer science, many ‘discoveries’ don’t hold up, about an oncology researcher trying to replicate some preclinical studies before moving forward with potential drug development. (thanks to a post via Branimir Vasilić http://goo.gl/wJyMx)

The news article summarizes a commentary in the journal Nature, titled, Drug development: Raise standards for preclinical cancer research.

Notice the difference in the titles? Here’s a similar discussion where Rajini Rao points out that the news article is titled, Eggs unlimited: an extraordinary tale of scientific discovery vs. Potential Egg Stem Cells Reignite Debate in the journal Science. Similar discussion here: http://goo.gl/Yq1ls

I want to focus on the oncology debate since I do cancer research. However, the comments from the article and me are relevant to many areas of research.

http://www.nature.com/nature/journal/v483/n7391/full/483531a.html

Drug development: Raise standards for preclinical cancer research

C. Glenn Begley & Lee M. Ellis

Nature 483, 531–533 (29 March 2012) doi:10.1038/483531a

Published online 28 March 2012

Here are 5 reasons why oncology research might not be replicated

Endpoints

As the authors point out, endpoints in cancer research can be less quantitative compared to say statin research where cholesterol level is the endpoint. In cancer studies sometimes tumor size is an endpoint. As an imaging person, my field very frequently frowns on this, as a drug can cause tumor swelling, i.e., increase in size, while actually causing tumor cell death. Not everyone has access to expensive imaging equipment or the skills to utilize many imaging modalities. So a lot of cancer drug researchers rely on caliper measurements of the tumor even though most would acknowledge that a tumor is rarely a perfect sphere where one only needs to measure the diameter.

Cutting edge

The authors suggest that some of the irreproducible results could be due to publications that were cutting edge, i.e., a researcher found something completely new or unexpected and published quickly. Also some technology might not be available to Amgen that was used in one of the publications. For example oxygen imaging is available in maybe 3-4 labs in the world.

Competition

Although this may sound terrible to the general public, there have been cases where researchers have omitted a key ingredient or step on a method in order to keep a competitive advantage.

Narrow scope

Begley and Ellis state that the robustness of some results were checked. For example, a publication might get phenomenal results with a particular tumor cell-line or model. When Amgen tried to broaden the scope, e.g., trying a different cell-line or model, the “narrow” promising results turned out to be less robust.

Statistics

Another issue is improper statistics. Quite often scientist haven’t had enough statistical training or do not consult a statistician and therefore use an incorrect method or interpretation.

Conclusion

Interestingly, Begley mentions that the results do not use enough predictive biomarkers (an area of focus for my research which I hope to contribute a solution). The authors’ suggestion to try to show tumor models where there is a negative result is often not possible when a grant funds a particular cancer or model. I totally agree about the selective presentation aspect of their paper. Unfortunately, I don’t think it is uncommon for a publication to have a figure that is stated to be “representative” of all the data, when in fact it was carefully selected as the best example. As some commenters on the online version of this Nature article state, it’s interesting that Begley and Ellis do not list the publications they tried to replicate, thereby limiting the possibility to replicated their article. Transparency?

Edit: I want to be clear that I don’t condone some of these reasons for the lack of reproducible publications. I want to emphasize that there are some reasons why a drug company might not be able to replicate a publication and therefore, there is no need for Reuters or Yahoo news to say the sky is falling for scientist.

For ScienceSunday

#sciencesunday #scienceeveryday