Posted: 18 Nov 2008 08:18 PM CST
Josh: We’re going to see an increase in sites like this where researchers from various disciplines can help each other out. This site has contact information for experts in various fields, allowing labs to more easily collaborate to do interdisciplinary research. I foresee sites like this becoming more “social”, where there are forums or means for researchers in one discipline to ask questions to experts in another discipline. It’s actually surprising that this doesn’t already exist, but I suppose most Web 2.0 technologies haven’t really been applied to other areas yet.
A world-first network linking experts in two leading biotechnologies, proteomics and metabolomics, has been launched by The Hon Gavin Jennings at The University of Melbourne.
The portal website of Proteomics and Metabolomics Victoria (PMV) was activated during the opening of Metabolomics Australia’s node at the University, and is now publicly accessible at www.pmv.org.au.
“Nowhere else is there a cross-sector network of this nature, involving collaboration between academia, trade and industry,” said Professor Mike Hubbard of the University of Melbourne’s Department of Paediatrics, who spearheaded the initiative.
PMV aims to provide education about proteomics and metabolomics, to help scientists access these technologies, and to facilitate practitioners’ interactions with the numerous companies supplying this field.
“Education and workforce development is a central concern shared by academic and commercial members, and together we aim to establish training schemes tailored to our collective needs.”
The State Government of Victoria supported establishment of PMV through funding of a proposal made jointly by Prof Hubbard and Monash University’s Professor Ian Smith.
Simply put, ‘proteome’ means all the proteins in an individual and ‘proteomics’ is the study of as many of those proteins as practicable.
Proteomics provides scientists with a variety of key benefits including deeper understanding of biological processes, increased diagnostic power, and access to information not available from gene-based approaches.
Similarly ‘metabolomics’ is the study of numerous metabolites, which are small molecules such as breakdown products of food, hormones and drugs.
Metabolomics provides scientists with several benefits that are both powerful in themselves and complementary to those of proteomics.
Through its link with the varied and dynamic nature of metabolism, metabolomics offers a very sensitive fingerprint for the status of a biological system (e.g. whether it is healthy or diseased or laden with performance-enhancing drugs).
Proteomics and metabolomics are used in many different research scenarios from academic laboratories in search of hot discoveries through to commercial applications in biotechnology, agriculture and medicine.
In the laboratory, these technologies are typically used to unravel basic biological mechanisms, details of which could lead to new understanding and ideas. Such “nuts and bolts” advances might in turn be harnessed by applications scientists to guide development of new drugs or diagnostics, for example.
“We hope to improve scientists’ access to proteomics and metabolomics, and facilitate interactions between the supply companies and practitioners of these technologies.”
“We also hope to give students and the public a clear understanding about our field, and illustrate its successful practice in Victoria.”
“The website showcases the depth of information and services available in Victoria.”
Source: University of Melbourne
Posted: 18 Nov 2008 03:29 PM CST
With apologies to Jonathan Eisen for encroaching on his annoyance specialty, here is yet another case of science via press release.
Big hop forward: Scientists map kangaroo's DNA
But check out the last line for the biggest problem in the story.
This isn't the first time Australia's unique wildlife has provided evolutionary clues. Earlier this year, scientists mapped the DNA of a platypus and found that it crosses different classifications of animals.
Posted: 18 Nov 2008 02:43 PM CST
Psst, you want eternal life?
In return they’ll give you back
Some of it will be plain wrong
If you’re at risk of getting fat
It’s personalised marketing:
Then, when you spend your precious time
Suddenly you’ll understand
Remind me now, why did you pay
Posted: 18 Nov 2008 01:27 PM CST
Posted: 18 Nov 2008 11:27 AM CST
The genetic engineering of humans is not yet a reality. But, with advancements in gene therapy and cloning, it will be. I think it is critical that Catholics be ahead of the rhetorical curve on this one, instead of behind. Now is the time to look at the genetic engineering of humans and what the Church says on the issue. Now is the time to understand what we as Catholics can embrace and what we should reject.
First, under the umbrella of "genetic engineering" we must make a strong distinction between gene therapy and genetic enhancement. These concepts are often confused and lumped together, but there are important moral differences.
For many years scientists have envisioned using gene therapy to cure devastating disease. Gene therapy would deliver a copy of a normal gene into the cells of a patient with defective genes to cure or slow the progress of disease. The added gene would produce a protein that is missing or defective in the diseased patient. A good example would be Duchenne Muscular Dystrophy or DMD. DMD is an inherited disorder where a patient cannot make the protein dystrophin which supports muscle tissue. DMD strikes in early childhood and slowly degrades all muscle tissue, including heart muscle. Average life expectancy is only 30 years.
Researchers have recently been able to introduce the normal gene for dystrophin in mice with DMD. They achieved this by inserting the dystrophin gene into the DNA of the mice. The genetically modified mice were then able to produce eight times more dystrophin than DMD-mice without the modification.
More dystrophin means more muscle which, in this case of a devastating muscle-wasting disease, is good. But apply this technology to a normal man who wants more muscle to improve his athletic ability, and you have entered the world of genetic enhancement. Genetic enhancement would take a otherwise normal individual and genetically modify them to be more than human in intelligence, strength or beauty.
Both are technically genetic engineering, but they have different intent and very different outcomes. Gene therapy seeks to cure disease. Genetic enhancement seeks to change the very nature of man: to make him "super-human." Those that that look forward to an age of human genetic enhancement are transhumanists. Humanity Plus is a transhumanist organization that wants everyone to "enjoy better minds, better bodies and better lives" and be "better than well."
It is with this distinction between genetic engineering as therapy and genetic engineering as enhancement that we must approach the advent of this technology. Confusion on this issue is common. For example, in his piece "The Vanishing Republican" in the New York Times, David Frum writes:
Frum believes that the Catholic Church would find genetic enhancement "laudable" as long as it was available to everyone. Is that true? Is that what the Church is really saying regarding genetic engineering?
Let us take a closer look. From Donum Vitae:
This passage clearly says that genetic engineering as a "strictly therapeutic intervention" is moral. So gene therapy is acceptable. But is genetic enhancement? This passage from the Charter for Health Care Workers sheds some light on genetic enhancement:
Once again this passage clearly states that gene therapy is morally acceptable, but it distinguishes between therapeutic manipulation and manipulation that simply alters the human genome for purposes other than curing genetic disease. I infer that gene therapy is a good, while genetic enhancement is morally troubled.
Also, this passage gives us guidance when it comes to germ-line modification. A germ-line modification is a modification to the genetic material of an organism in such a way that the modification is inheritable. This can be done by modifying sperm or egg before in vitro fertilization or by altering or adding genes while cloning a human embryo. Adding an extra muscle building or intelligence enhancing chromosomes to the normal genome, and then creating a human embryo with the extra chromosome, would produce a genetically enhanced child.
This is genetic engineering at its worst. Not only would the child have no choice in being genetically modified, but also the modification would extend to his or her eggs or sperm. The modification would be "permanent." A genetically modified human being would have no choice but to pass the modification on to their offspring. This is exactly what the Church is referring to when it talks about manipulating the "the human genetic patrimony."
A germ-line genetic enhancement would result in a modification of an entire human organism, including its sperm or egg cells. Gene therapy would only genetically modify the diseased tissue and therefore would not be an inheritable alteration.
Some would argue there is only a hair's difference between gene therapy and genetic enhancement and with one will come the other. We must fight this thinking for two reasons. One, because genetic engineering will no doubt have unintended consequences and unforseen side effects. It should only be under taken in cases where the benefits will outweigh the risks, as in the treatment of life-threatening illness. Genetic engineering should never be used on an otherwise healthy person because the risk is not worth the so-called "reward."
Secondly, because it is important to embrace ethical technology whenever we can. Catholics often knee-jerk against any biotechnology painting it all as unethical. This not only ignorant, but it allows others to label us as uncompassionate Luddites. We must make a distinction between gene therapy and genetic enhancement so we can reap the rewards of genetic research while rejecting the push to fundamentally change humanity.
Posted: 18 Nov 2008 11:14 AM CST
I’ll be guest blogging for the next four weeks at Biotech and Beyond, an Invitrogen-sponsored blog hosted by ScienceBlogs. Check out my first entry:
Update: As usual, I’m early to the party. Biotech and Beyond isn’t officially live yet as it’s awaiting a banner from Invitrogen. /banghead
Posted: 18 Nov 2008 10:42 AM CST
In our last episode, I wrote about embedding Google forms in my classroom wiki pages.
Recently, we've been working on a project where students enter results into a Google Docs spreadsheet, via our classroom wiki. All the students were able to enter their results.
Except for one.Read the rest of this post... | Read the comments on this post...
Posted: 18 Nov 2008 10:18 AM CST
A Nature News article discusses the ongoing 1000 Genomes Project, an international effort planning to sequence 1,200-1,500 human genomes. The discussion springs from project co-chair David Altshuler's update at last week's American Society of Human Genetics meeting on the progress of the project (in brief: 3.8 terabases down, 996.2 terabases to go).
The article provides a generally positive overview of the project's historical context, goals and progress. The one contrary note comes from Duke University's David Goldstein, who has previously publicly expressed skepticism regarding the value of much of the data currently emerging from genome-wide association studies looking for common variants underlying common disease risk. Goldstein is also wary about over-stating the importance of the 1000 Genomes data:Read the rest of this post... | Read the comments on this post...
Posted: 18 Nov 2008 07:18 AM CST
Yesterday, Australian researchers at the ARC Centre of Excellence for Kangaroo Genomics (KanGO) announced that they have built a framework to assemble the genome of a model kangaroo, the tammar wallaby. KanGO Director Prof. Jenny Graves stated: A good map is crucial for finding our way around a new genome. It enables us to explore how the [...]
Posted: 18 Nov 2008 06:00 AM CST
Scienceroll is 2 years old today. I’m very happy because medical blogging gave me so many things, opportunities and friends. This year was definitely dedicated to Webicina.com, my service that aims to help patients and physicians enter the web 2.0 world. I also listed some of the achievements of these 2 years.
Dear readers, I hope you will follow me for at least another year. I will be here…
Posted: 18 Nov 2008 05:29 AM CST
We trust health assets like “medical advice” to exist. That is, we trust that public medical information describes reality such that it may be applied to measurably improve health. This is a challenge because medical advice, especially preventative medical advice like genomics, is a trust asset: an abstract idea with value applied to the indefinite future. However, that trust is under attack, and as the immediately profitable but eventually catastrophic erosion of the term “insurance” now jeopardizes the financial industry, the meaning of term “medical advice” is now being eroded by greedy companies. Why is the meaning of “medical advice” so important to medicine, and why is this trusted label so vulnerable in America when other types of asset labels are so well protected?
Immediate reality enforces the existence of a physically realizable asset like a good or service. The owner enforces the existence of an abstract asset like a brand or copyright. But who enforces the existence of a socially understood trust asset like medical advice? Apparently, nobody.
The value of physical asset like a steel rail is obvious because its meaning is self evident. The value of an abstract asset like a brand is generally obvious because its meaning is generally self described. Most products in a marketing economy are meant only to please, and if they do not, they may be returned for a refund. But if its meaning is ambiguous, who can judge the value of a trust asset like medical advice? Apparently, since products purported to improve health are not held to any rational standard to improve health, nobody.
Finally, to mislabel a physical asset like a steel rail as “this is not a steel rail” is of little threat because that is absurd. To mislabel an abstract asset like “Pepsi” is extremely illegal because that could be believed. The meaning of an abstract asset is self described, and if a label is allowed to be ambiguous, then meaning of that label is destroyed. But when a label of trust is arbitrarily applied —derivative, insurance, medicine— nobody knows what to believe, and all trust assets of that label are destroyed. No trust, no value, no asset.
Does “medical advice” exist, or does it not? Does “medical advice” mean “information to be applied for better health,” or does “medical advice” mean “I have or have not explicitly labeled this information as medical advice”? Does medicine describe physical reality, or is medicine an arbitrary legal term to be ignored when commercially convenient? Are you using medical science to predict future health, or are you making money now because in the future… well, “that’s business”?
It happened in finance, it is happening in medicine, and now we have allowed the most promising new field of medicine, genomics, to be predicated by it.
Is this what we want? For genomics to be the “credit swap” of medicine? We allowed words like “insurance” to become nothing more than an optional label of legal liability, and the resulting disaster now threatens the very meaning of finance itself. And now that Old Wall Street is rubble, companies like Navigenics want to found genomic medicine as New Wall Street. Is that what “medical advice” is? An optional label of legal liability? And who is trying to stop them? You? Anybody? Nobody. Have a brochure. Invite everybody to your conference. Revel in the celebrity! Woopie! You don’t want to miss the foundings and fortunes of new Wall Street! Just wait until “health” can be traded as an asset! Oh boy!
It’s not enough in science —it is not enough in medicine— to “do no harm.” The meaning of medicine must be defended. When we are convinced that cleaning solutions will make our bathrooms “sparkle” because “cute animated scrub brushes fly around on TV,” we can forgive that. When the leading American industry is the ability to convince ourselves in 15 seconds to our spend per capita GDP on a car because “explosions,” we let that slide. These are obvious, physical assets, and they are either purchased, or they are not, and “no harm is done.” In fact, you might feel better about cleaning your bathroom, and your improved apparent socioeconomic status may help you date more attractive people. Congratulations.
But medicine is trust, and when preventive health care is labeled, marketed, and sold like branded “insurance that is not insurance,” that must not be tolerated.
Truth is not a marketing expense. If you are a physician or a scientist and you would like to someday use medical science to compete for the attention of the public with others wielding cartoons and explosions, ignore me. If not, then act.
Posted: 18 Nov 2008 04:25 AM CST
~Submitted by: Jeff Brown, astronomer, Bloomington, Indiana
Which one are you? The weirdo or the smart-aleck?
via Rules of Thumb
Posted: 18 Nov 2008 04:22 AM CST
Following up on my recent post about The Nature of Scientific Observation, I left two-thirds of Chalmers’ book What is This Thing Called Science untouched, including discussions on Bayes’ theorem and the New Experimentalism.
I left off right before Popper’s falsificationism and Kuhn’s paradigms came into view. Each of them has their own problems. Popper, for instance, introduced the falsificationist concept with simplistic examples that the actual scientist rarely encouters. Nevertheless, Popper’s Logic of Scientific Discovery does seem to reflect some of the approach that the typical scientist has been taught to apply in formulating testable hypotheses. As a result, sophisticated falsificationism takes a somewhat defendable position by reiterating falsificationism in strongly qualified statements.
Thomas Kuhn then introduced scientific revolutions as “paradigm shifts”, exposing the hard truth that science is normative. No argument there. But the problem lies in the logical conclusion that many people draw from the realization that science is normative: science is therefore more subjective and more falliable than we originally may have supposed, and pseudoscience might find comfort in the doubt sowed in science therein. Kuhn simply could not reconcile his normative description of science with what is obvious to any empirical scientist, which is that many scientific theories can explain wide ranges of natural phenomena with a high degree of precision. In other words, though science may be normative in practice, it is also grounded in high-level approximations of reality, and basic facts exist which can be said to be objective.
As a result, I characterize Kuhnsian paradigms as not a philosophy of science, but a sociology of science. That view has gotten me in some strongly-worded discussions with other scientists, but it’s a position that I stick to. It is very clear that some theories are better than other, and that science does indeed represent progress. One needs only to look to the offspring of science, technology. Advancements in biomedical, mechanical, electrical, and chemical technology are not mere paradigms.
Enter the Bayesian theorem of science and the New Experimentalism.
Thomas Bayes, an 18th-century mathematician, established a theorem that has a great deal of bearing for philosophy of science. Bayes’ theorem is about conditional probabilities, which prescribes how probabilities of truth statements are to be changed in the light of new evidence. Chalmers describes, on page 175:
This symbolic calculus serves to illustrate that any disagreements in science between proponents of rival research paradigms or programs must have their source in the prior probabilities held by those scientists, since the evidence is taken as given and the inference considered to be objective. But the prior probabilities are themselves totally subjective and not subject to a critical analysis.
Consequently, those who raise questions about the relative merits of competing theories and about the sense in which science can be said to progress will not have their questions answered by the Bayesian. Bayes’ theorem of science does, however, reflect the importance of the relevance of new data. That is, empirical evidence is not all considered equal - some evidence is strongly weighted as far as importance goes, whilst other evidence is considered irrelevant.
The New Experimentalism is an intriguing contrast. Chalmers starts off with an example (an experiment by Michael Faraday on electromagnetism) and then asks (page 195), “Is it useful or appropriate to regard this accomplishment of Faraday’s as theory-dependent and falliable?” Without question we can say that, at best, one can only refute the extreme empiricist position that facts must be established directly by the entry of sensory data into a mind that otherwise knows nothing, and that the recognition of a new experimental effect cannot be said to be falliable in any sense.
Thus, the production of controlled experimental effects can be accomplished and appreciated independently of high-level theory. Molecular biology is replete with examples of experimental observations that are tightly controlled, and the results derived therein can be considered objective. Extrapolating from those observations to theoretical implications is not always straightforward, to be sure, but possible if the experiment itself has relevance to aspects of those theories which are in contention among scientists.
Deborah Mayo offers the best articulation of the New Experimentalism in her 1996 book, Error and the Growth of Experimental Knowledge. She sides with Kuhn’s notion of normal science, reformulating it in such a way that reflects the ability for scientists to make factual statements independent of theory, even though they remain subjective and fallible to a degree.
So I found myself nodding very much through reading about Deborah Mayo and the New Experimentalism. I am surprised that I hadn’t read much about this area of the philosophy of science before.
Overall though, I think it also helpful to note that each of the major philosophers of science tackle a separate aspect of science - how hypotheses are made; how science is normative; the role of inductive and deductive logic; how experiments are formulated; how facts and theories are inter-dependent; etc. Each of them has a point, but none of them can be extrapolated to science as a whole.
Posted: 18 Nov 2008 01:00 AM CST
Security of genetic information is an enormous concern for individuals, and thus an enormous concern facing commercial genetic enterprises. I was recently having a conversation with someone about the security of genetic and personal information at companies such as 23andMe and Navigenics, and I pointed out that the very livelihood of these organizations depends on their ability to secure information. A single security breach could potentially drive away future customers.
The moderator of the discussion was Hank Greely, a professor at Stanford whose work I highly respect and enjoy.
A recording of the panel discussion will be made available here at some point in the future.
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