Posted: 29 Oct 2008 08:00 PM CDT
Coast to Coast Bio is a podcast that will evolve over time, but it’s a couple of geeks, who don’t always agree on things, bantering about biology, programming and all kinds of stuff. You might see a screencast or two in there as well. Episode 1 went live today. Still rough around the edges, but hopefully will tighten up as our workflow gets more streamlined.
Posted: 29 Oct 2008 07:09 PM CDT
Posted: 29 Oct 2008 06:42 PM CDT
I know, I have been away for a long while, but I am now back in broadband county, and able to blog again. I am thinking of starting a podcast, but I am uncertain about whether you would prefer listening to the Skeptical Alchemist, or keep reading my posts -- so I have posted a poll on the right column of the blog. Let me know what you think!
Also, thanks to all those who have stuck around, and apologies about the Molecular and Cell Biology Carnival -- it will be up and running again very soon, as i have seen that some of you even submitted during the summer!
I have a couple of DVD reviews overdue from the beginning of summer, but before I get to that, I would like to concentrate on an issue that I found particularly worrying, and that was raised, like so many others, by the speeches being given during this US Presidential Election.
Very recently, Sarah Palin criticized the use of public money for the funding of fly research, adding a smirk and suggesting to the American public that this research has no public utility, and therefore no public money should go and fund it. Similar remarks were made by the Republican presidential candidate, John McCain, regarding the study of bear DNA.
Here are two clips of their public remarks.
First comes Sarah Palin and her personal view of (French?) fruit fly research [link]
Then comes McCain and those beloved bears [link]
Of course, the best part of all this is that Sarah Palin initially supported funding for the famous "bridge to nowhere", and McCain himself voted for the bill that allowed $3 mil to be spent to study the DNA of those same bears.
Now, the main concern here is not that these politicians are lying: the main concern is that they can easily point to these as "earmark spending" and unnecessary spending because the American public has no clear understanding of how science research works, and what its function is. Even more problematic, is that the politicians themselves, who are supposed to guide spending, have a flimsy understanding of how research money is allocated (competitive grants) and why basic research is conducted on model organisms. Sarah Palin supports research on autism....and then is not aware that basic research on autism is also conducted on fruit flies!
We could, of course, run tests and basic research directly on the victims - that would surely be of public utility... oh, wait, I just remembered that model organisms are used because doing this research on humans is unethical, and organisms are carefully chosen on the basis f their similarity with humans with regard to the molecular interactions and genetic abnormalities studied...
The statements above suggest that the victory of the Republican ticket for the White House will most probably severely hit basic research funding, while still fueling billions of dollars on the questionably successful war in Iraq. I hope that American voters will come out in force and vote for science, basic research, and against obscurantist views like those portrayed by the current Republican ticket.
And before I go... should I remind voters that the useless particle physics research led to the invention of the Internet, which is now abundantly used trying to discredit more basic science research, including the latest CERN projects?
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Posted: 29 Oct 2008 06:39 PM CDT
Somehow medical professionals tend to order Medicine 2.0 Packages while patients do not. The mission of Webicina is to open the world of web 2.0 not just for doctors and nurses, but for patients as well. That’s why we will dedicate the month of November to patients with new prices and opportunities.
Medicine 2.0 Package is a personalized set of web 2.0 tools designed to solve your problems.
Such a package contains all the quality blogs, blog carnivals, community sites, video sites, microblogging sites, search engines, slideshows and many many more tools/services/websites that focus on one medical condition or medical specialty.
Details on the Webicina blog.
Posted: 29 Oct 2008 04:55 PM CDT
Take that, you “vote-yes-on-proposition-8″ hate-mongers. The Economist reports: genes that make people gay also make their siblings more fertile. It’s the genetic equivalent of a lateral pass in football. (Image courtesy of The Metrosexual Tarot)
Posted: 29 Oct 2008 03:02 PM CDT
If you're in the Indianapolis, Indiana area on November 10th, join us at the IU Center for Bioethics with Mark Stranger, Ph.D., from the University of Tasmania. Our guest will be delivering a talk on Genetics, Ethics and the Law Down Under: A Tasmanian Perspective from 3:00-4:00PM in the HITS Building, Suite 3100 [Flyer - PDF 74 KB]. Dr. Stranger, a sociologist with expertise in risk assessment, social change, biobanking and social research methodologies, is a Senior Research Fellow and Executive Director for the Centre for Law and Genetics at the University of Tasmania. He also manages the Centre's multidisciplinary and international Biotechnology, Ethics, Law and Society Network.
This event will be convened by the Indiana University Center for Bioethics; IUPUI Consortium for Health Policy, Law and Bioethics; and the IUPUI Office of International Affairs. - ALG
Posted: 29 Oct 2008 01:26 PM CDT
Nature has an editorial (America's choice : Article : Nature) on the US Presidential Election that is worth looking at. For those interested in the Cliff Notes Version they end the piece with
"This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama."For more detail, I think the key point is here:
On a range of topics, science included, Obama has surrounded himself with a wider and more able cadre of advisers than McCain. This is not a panacea. Some of the policies Obama supports — continued subsidies for corn ethanol, for example — seem misguided. The advice of experts is all the more valuable when it is diverse: 'groupthink' is a problem in any job. Obama seems to understands this. He tends to seek a range of opinions and analyses to ensure that his own opinion, when reached, has been well considered and exposed to alternatives. He also exhibits pragmatism — for example in his proposals for health-care reform — that suggests a keen sense for the tests reality can bring to bear on policy.They basically reiterate my concern for the McCain-Palin platform regarding science but they do not really go far enough. McCain and Palin have expressed decidedly anti-science positions recently (well, Palin has expressed them previously too). And thus it is not simply what advisors they surround themselves with but whether they would listen to any of them. Sadly the hints are that McCain and Palin will not listen to scientific advisors on many issues. Obama has made it clear that he will. Not that he puts science above all else (nor should he) But at least he will listen and make rational decisions that include science as a component. McCain and Palin seem dead set against "evidence" of any kind much of the time (note - McCain still exhibits occasional glimpses of the reasonable person he used to be on some issues like Global Warming - but these are few and far between).
Hat tip to Oliver M. for sending this around ...
Posted: 29 Oct 2008 12:16 PM CDT
"Yes," argues Team 1. "It is better to invest in more tests now rather than pay for a mistake later. Despite the clear benefits of GE crops in reducing insecticide use, the long-term effects are impossible to predict. Therefore it is best to put off commercialization. A longer period of safety testing will relieve public concerns."
Team 2 did not agree. "We need the benefits of GE crops now. People are dying from hunger, malnutrition and pesticide poisonings- not from GE food. It is a waste to spend more money on testing to teach the public about what is already known. Further testing would further delay the changes needed on our farms. If we ban GE crops then there will be less food available globally, which will increase food prices here and abroad. Think about your average college student who cannot afford organic food. Then think about the poorest people in the world; they cannot afford more testing. What is enough safety testing and who defines the limits? After 12 years of testing, without a single instance of harm to human health or the environment, and the support of 25 Nobel Prize winners, it is clear that GE crops are safe and beneficial."
Team 1 responded, "Just because GE crops are safe now doesn't mean that they will be safe later. What if new allergens form from the gene that has been inserted? What if farmers only cultivate one variety of GE crops and nothing else? That will diminish genetic diversity and make the crop vulnerable to potentially devastating diseases. Think about the Irish potato famine where the entire crop was killed by a fungal pathogen. Hundreds of thousands of people died and many more emigrated."
Team 2 pointed out that GE food must be labeled if the gene is derived from any of the common allergic reaction- inducing food such as peanuts or wheat. "It is similar to what is written on your cereal box-' This product was processed in a facility that uses peanuts' ".
This is the third in a series of debates conducted by undergraduate students in the class "Genetics and Society" at the University of California, Davis.
Posted: 29 Oct 2008 10:49 AM CDT
In all the fervor over whether or not Senator Obama supports infanticide by not voting for legislation that would protect infants born-alive after an abortion, it is easy to forget that the children that are being aborted often have Down Syndrome.
Somehow, someway, as a society we have embraced the idea that death is a solution. From assisted suicide to late-term abortion to pre-implantation genetic diagnosis, the premise is the same: Death is a treatment for a difficult medical problem that at this very moment in time does not have a cure.
Unfortunately, that is so short-sighted and frankly ignorant. Especially in the cases where genetically "defective" children are being thrown away in IVF clinics or even aborted alive and then allowed to suffocate to death, because the assumption is that if there is nothing doctors can do now, then there will be nothing in 10, 20 or 50 years.
Paradoxically, the same society is putting all of its hope in scientists and doctors to make sure those of us who did make it out of the womb alive get to live forever.
I came across this study to treat symptoms of Down Syndrome, and was reminded that there is no hope in death. There is no hope for a Down Syndrome child who is ripped from his mother's womb, never to be enrolled in a clinical study, never to be offered treatment.
Remember: abortion, assisted suicide and pre-implantation genetic diagnosis don't cure any disease or disorder. They only eliminate the people that have them.
Posted: 29 Oct 2008 09:23 AM CDT
Kristen West with the University of Alabama at Birmingham, Department of Genetics talks about genetic services offered at UA
Joi Morris speaks about FORCE, a national organization that provides support for women and families with inherited breast ans ovarian cancer.
You can follow the Youtube channel of Chavonne here.
Posted: 29 Oct 2008 09:11 AM CDT
This is the 5th week of my Medicine 2.0 university credit course. Now I posted some material and a few images as well on the blog of the course.
This week, I will talk about the world of e-patients and medical communities.
Posted: 29 Oct 2008 08:07 AM CDT
Posted: 29 Oct 2008 07:29 AM CDT
Tip to Dr. Steven Murphy for bringing this article to my attention. He notably accompanied his email with much more profanity than I will use in this post.)
Note this excerpt from the deCODEyou blog October 20th: Customer Story: The Path To Prevention: (emphasis mine)
In other words, while putting everyone on a monitor for a month would catch more heart attacks, it’s not a “feasible” allocation of resources. So, the deCODEme test, which as stated has no evidence, is being used like a random number generator to justify picking some patients for additional care and not others. Why? They tested positive for the A-fib gene. Magic.
So, since there is no evidence, only “decision to take action,” you could replace the deCODEme test with a homeopathic test that produces the same ratio of positive results for the same clinical effect. I understand that people sometimes feel they need a special reason to pursue healthcare from which they could always hypothetically benefit, but there is no rational necessity to produce this impetuous prior to treatment other than the psychological comfort of rationalization.
I would like to see a study where one person gets the genetic test, and one person gets a random jibberish report recommending the same thing, and see if there is a clinical difference. Random jibberish is much cheaper to produce. Why not save your money and get a random jibberish test to help you “decide to take action?” I will put it in a leather case and have a doctor sign sign it on real parchment and read it to you in a very authoritative tone and use big words. You will be 238.8% as decided to take action as if I posted the result on your genomic Web 2.0 deCODEme profile. (there is no evidence to back this claim)
Non-casual risk testing at low-mid penetrance like deCODEme has great potential someday, but only to more optimally ration scare health resources for better net efficiacy that otherwise should be provided to everyone. However, there is no shortage of “eat healthier, reduce stress, exercise, and see a doctor if you have a problem” which is the best medical recommendation that can be produced by today’s DTC testing.
On an individual scope, one must ration personal wealth to pay for healthcare. It’s feasible that low-mid penetrance can aid in making more rational decisions. However, it’s much more likely that personal decisions to pursue which healthcare strategies are in no way rational or scientific and that “optimization” is a delusion. You can’t perform risk benefit assessment arithmetic on “your feelings.” 20% + you’re scared isn’t a number with a dollar sign.
On a social scope, low-mid penetrance risk assement can help better allocate a fixed amount of resources per person to purchase the most personally effective healthcare. However, this is assuming that the healthcare industry isn’t corrupt and would use the tests to justify whatever medically-arbitrary decision they’ve already made to benefit themselves. I don’t think that assumption is justified until the medical benefits of these tests are so obvious as to prevent such bureaucratic abuse excused as an “ongoing discussion.”
But, by all means, buy a deCODEme test. It’s the American way. But do it because you want it, not because of some magic you wish was medicine because you’re afraid of illness and death.
Posted: 29 Oct 2008 07:00 AM CDT
History teachers can always turn to the significant figures and battles to enliven their lessons, biology education has the enormously diverse range of species to point to, and even physics can pull in metaphors and anecdotes for the more esoteric aspects, try teaching gravity without mentioning Galileo and the Leaning Tower of Pisa. But, teachers of mathematics have it tough. They can describes solids and shapes, discuss how Alice and Bob might share out an apple pie fairly between nine friends. But. How does one visualise an abstract equation like this:
A rare few students will cope entirely, finding a way to see what such a formula means, but most struggle (I know I did) to imagine an object like a four-dimensional hypercube, for instance.
Annunziata Cascone, Gerardo Durazzo, and Valentina Stile of the Department of Information Engineering and Applied Mathematics, at the University of Salerno via Ponte don Melillo, in Italy, point out that mathematics obviously plays an instrumental role in technical degrees, science, engineering, computing etc. Moreover, given how common is the use of computers and calculation programs today in these areas it really is critical that students can get to grips with seemingly esoteric mathematical concepts that have direct application but are hard to visualise.
The team suggests that Computer Algebra Systems (CASs) are the way forward in teaching mathematics for engineering and other technical subjects. Unfortunately, there are many professors who hesitate to use such technologies. They cite technical, personal or even political reasons, Cascone and colleagues explain. “An explanation for such behaviour can be found in the fact that most teachers were not taught to use CASs when they were studying to be teachers,” they say, and so perhaps don’t recognise the enormous possible benefits.
Writing in the International Journal of Knowledge and Learning this month, Cascone and colleagues describe an approach that can effectively integrate CASs into an analysis course, which they say can improve students’ conceptual understanding significantly.
To improve students’ ability to make some geometric concepts concrete, we developed a Mathematica package that is able to realise and visualise the result of a plane domain revolution in a three-dimensional space.
In other words, the package can generate pictures and computations for an equation that would otherwise not have its significant figures, events, battles, and apple pies. “CASs, when used thoughtfully, allow students to concentrate on conceptual development,” the researchers say, “The same students claim that the use of CASs created the possibility of checking their paper-and-pencil results; it enabled them to discover their mistakes and it clarified the processes to solve problems.”
Annunziata Cascone, Gerardo Durazzo, Valentina Stile (2008). Solids by revolution: materialising an idea International Journal of Knowledge and Learning, 4 (2/3) DOI: 10.1504/IJKL.2008.020651
Posted: 29 Oct 2008 05:09 AM CDT
Currently I’m reading Alan Chalmers’ What is this thing called science?, with specific interest in the questions of expertise and the uniqueness of science as a foundation for knowledge. (Coturnix’s recent post on Information, Knowledge, and Experience helped crystallize my thoughts - check that out as well.)
Philosophy of Science has come a long way since the days of Popper and Kuhn, and I was suggested to read Chalmers about six months ago. This is a very good book, clear and well written, and provides an excellent overview of philosophy of science (including all the major players: Popper, Kuhn, Lakatos, Laudan…) and the problem of demarcation between science and non-science.
I haven’t yet reached the chapters on Bayesianism and New Experimentalism. Most philosophers of science share concerns about falsificationism versus verificationism (or deduction versus induction) - and Bayesianism and Experimentalism provide some sort of response to these concerns, or so I’ve been told.
The opening chapters however nicely clear away some popular misconceptions about science, by contrasting what science is with what it is not.
Chalmers is tearing down the notion that the acquisition of facts precedes the formulation of laws and theories. While many scientists may not care much about philosophy of science, and assume that facts come before theory, all scientists at least implicitly understand this situation.
While science is in part a method, it is also an ediface of knowledge that acts as a starting point for discovery.
In the specific case of the molecular biologist, every hypothesis and experiment is founded on volumes of information which must be assumed. It is, in fact, falliable to some degree. How than can science be made more reliable?
I read this as a strong rationale for not just standard modes of knowledge dissemination such as the published literature and attending symposia, but for the extreme case of Open Science. That is, the greater the transparency and openness of the discussion over relevant data, the more objective we can claim the current state of scientific knowledge.
This is the pragmatic empiricist position, that science is not exclusively inductive or deductive. It is, in fact, quite a bit of both. And again, neither can operate in a vacuum free from pre-supposed knowledge.
Which brings me to a passing note on creationism, which seems to misrepresent or ignore the existing body of literature. And those few creationists who do attempt to insert their inductions into the scientific literature (e.g., Stephen Meyers and Jonathan wells) have completely refused to do anything deductive to back up their fundamental inductive observations. That is, the falliability of their observations cannot be seen independently and corroborated practically.
Thus far, the What is This Thing Called Science has been more about what science is not however. I can’t wait to get to some more intruiging sections about what science is - and New Experimentalism and Bayesianism in particular. Be sure to check back.
For more: Biology and the Scientific Method.
Posted: 28 Oct 2008 10:41 PM CDT
This looks really interesting. The goal is to use whole genome SNP data to predict three phenotypes in mice (coal color, % of CD8+ cells, cellular hemoglobin), using "reversible jump MCMC". According to this website this is how RJMCMC works:
"– RJMCMC randomly "walks around" the space of possible model structures by changing one edge at a time – called structurallearning.They cite this recent paper that I posted about a few months ago that proposes a different way of looking simultaneously at the association between a collection of SNPs and some trait.
So, in this paper, they seem to be able to make decent predictions about these traits using about 12,000 SNPs in each of 2,300 mice. The correlations between observed and expexted phenotypes, using only genotype data, are in the range of .33 to .85.
There's really a lot of interesting things in this paper and I don't have to go over all of them.
I'll just end by mentioning that, as the authors state, if we were to do this in humans we would probably need many more markers and more individuals since the mice used in this experiment were from inbred lines with extended LD.
Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data
Sang Hong Lee, Julius H. J. van der Werf, Ben J. Hayes, Michael E. Goddard, Peter M. Visscher
PLoS Genet 4(10): e1000231.
Abstract: Genome-wide association studies (GWAS) for quantitative traits and disease in humans and other species have shown that there are many loci that contribute to the observed resemblance between relatives. GWAS to date have mostly focussed on discovery of genes or regulatory regions habouring causative polymorphisms, using single SNP analyses and setting stringent type-I error rates. Genome-wide marker data can also be used to predict genetic values and therefore predict phenotypes. Here, we propose a Bayesian method that utilises all marker data simultaneously to predict phenotypes. We apply the method to three traits: coat colour, %CD8 cells, and mean cell haemoglobin, measured in a heterogeneous stock mouse population. We find that a model that contains both additive and dominance effects, estimated from genome-wide marker data, is successful in predicting unobserved phenotypes and is significantly better than a prediction based upon the phenotypes of close relatives. Correlations between predicted and actual phenotypes were in the range of 0.4 to 0.9 when half of the number of families was used to estimate effects and the other half for prediction. Posterior probabilities of SNPs being associated with coat colour were high for regions that are known to contain loci for this trait. The prediction of phenotypes using large samples, high-density SNP data, and appropriate statistical methodology is feasible and can be applied in human medicine, forensics, or artificial selection programs.
Posted: 28 Oct 2008 10:27 PM CDT
Just a quick one here. All those interested in Open Access should look at this editorial on PLoS Biology from the PLoS Biology staff PLoS Biology - PLoS Biology at 5: The Future Is Open Access
Posted: 27 Oct 2008 09:37 PM CDT
Michael Nierenberg, M.D.
Crohn’s disease isn't something that usually comes up in cocktail party conversations. It isn't featured prominently in television shows or radio spots. Ask your average person what Crohn's is, and they likely will be hard-pressed to give you the right answer.
But this chronic inflammatory bowel disease is featured on the Web site of the New York Times, putting a face – or faces, in this case – to this rarely discussed disorder. In this interactive feature, seven people ranging in age from 19 to 61 share their experiences with the condition that has been diagnosed in more than 300,000 Americans.
"It takes forever to get diagnosed with Crohn's," recounts Ryan Walsh Horowitz, 19, of Brooklyn. "They thought I was anemic. They thought I had leukemia – and a bunch of other things."
That is not surprising, nor an isolated problem.
Crohn's has long been overlooked or misdiagnosed in the general public. The most common symptoms are, well, common: diarrhea, constipation, gas, abdominal pain, bloating and loss of weight. So it's easy to see why many other health conditions are often suspected first.
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