Posted: 07 Oct 2008 04:56 PM CDT
After months of hard work, today we launched Webicina officially, an online service that aims to help medical professionals and patients enter the web 2.0 era.
Please visit our site and register to get access to the free e-courses and to see what kind of services we provide.
The first steps of e-courses you can access now for free:
And feel free to join the discussion about how to change the way medicine is practiced and healthcare is delivered with web 2.0 tools.
Timeline of Webicina:
The site was designed and constructed by Gergő Vargyai. Many thanks to him for the great work!
Posted: 07 Oct 2008 01:54 PM CDT
According to this paper in the journal of sexual medicine, premature ejaculators have lower levels of serotonin in the parts of the brain that control ejaculation. In fact this serotonin difference can even be seen in a rat model of premature ejaculation:
"When large populations of male rats are tested on sexual activity during four successive tests, over time individual rats display a very stable sexual behavior that is either slow, normal or fast as characterized by the number of ejaculations performed. These sexual endophenotypes are postulated as rat counterparts of premature (fast rats) or retarded ejaculation (slow rats)."
Since this is clearly not psychological, and conserved in other species, it makes me wonder if in fact evolution hasn't positively selected it. I could see it being a survival advantage in an illicit encounter, since it leaves more time for flight. All this to introduce the best quote of the week:
She said men with primary premature ejaculation tended to be fast reactors generally.
"These men have very quick reflexes. They may be excellent at playing tennis or computer games, for example."
Posted: 07 Oct 2008 11:01 AM CDT
Got to run but thought people might be interested in this story. See the scoop at Scientific American. Will post more later. Open access publisher BioMed Central sold to Springer: Scientific American Blog
Posted: 07 Oct 2008 11:00 AM CDT
Seth Godin writes
But this should come with a big caveat: it better be right around the corner, otherwise when the corner comes, and nothing is to be found, you lose all credibility. As a product manager, I was never a fan of date driven releases, especially in a traditional software shop. What you need to figure out is the core set of functionality (not features) you want to provide, and start executing. When you are comfortable with the project start setting expectations with your customer base.
Posted: 07 Oct 2008 10:15 AM CDT
Rosie Redfield has an agonizing and interesting series on her blog about her attempts to pay for an article of her's coming out in the Journal of Molecular Biology to be "Open Access" under the Elsevier OA option (note - this is not fully OA, but it is better than the standard option for this journal). Here are some of her postings worth looking at:
Rosie is one of the true pioneer's of Open Science, as she has turned her blog into a form of open notebook where she posts discussions about her current research, her papers in progress, grant proposals, and other ideas. Yet the process of trying to pay Elsevier to make her article somewhat more open, and the confusing way "Open Access" is presented by this journal has caused Rosie to (1) give up on the open option for this article and (2) become possibly more enamored with journals that are a bit more committed to Open Access from the beginning.
In her latest post she says
"The Elsevier sponsored-access system is confusing, the policy is not clearly explained, and the necessary information is hard to find.
Posted: 07 Oct 2008 10:00 AM CDT
Roberta Weiss, a nephrologist (kidney doctor) emailed to provide Sciencebase readers with some more background on melamine toxicity. Weiss suggests that, “Probably acute renal failure resulting from cyanuric acid crystal formation in the kidneys of babies that ingested the melamine contaminated formula was responsible for the infant deaths, not kidney stone formation.”
Weiss is a kidney doctor for adults, but emphasises that she has never seen a case of melamine related kidney or bladder stones. However, there have been animal studies carried out since the 1980s that do demonstrate that the ingestion of melamine by mice can cause bladder stones, known technically as urolitiasis. These are apparently associated with ulcerations in the bladder. Weiss adds that the animal food tainted with melamine that killed so many pets in the US contained products in the feed from China.
As I’ve mentioned here before, melamine is an organic compound used in the manufacture of plastics and fertilizers. It releases cyanide when burned and has been associated with cyanide poisoning in industrial accidents. Melamine monomer, as opposed to the plastic used to make kitchen utensils and table coverings, itself also has irritant properties. It has been added to various food products to illicitly and fraudulently boost the measured protein content without the expense of actually improving the food’s nutritional value.
According to The Register, Chinese company, Xuzhou Anying, was advertising “dust of melamine” as something it called “ESB protein powder” on the global market trading website, Alibaba. “The latest product, ESB protein powder, which is researched and developed by Xuzhou Anying Biologic Technology Development Co., Ltd… Contains protein 160 - 300 percent, which solves the problem for shortage of protein resource,” it boasted. A horrifying thought, makes you wonder what is actually in those nasty protein powder drinks bodybuilders use.
“Melamine ingestion results in the production of cyanuric acid in the kidneys,” adds Weiss, “which results in intratubular crystal formation and acute renal failure.” This, she explains occurred in cats who were fed melamine in combination with cyanuric acid experimentally after the pet food issues to demonstrate what may have been happening during that incident.
According to Economics And Finance (Cai Jing) magazine, as reported in the Epoch Times, it is common practice to add melamine to livestock feed along with sodium nitrite, urea, ammonia, silica, potassium nitrate, sodium nitrite, glacial acetic acid, activated carbon materials, urea, ammonia, potassium nitrate, to improve its nutritional profile and other properties of the feed. The use of melamine in this context contravenes international regulations where they exist.
The UN Food and Agriculture Organization (FAO) points out that, “Regulation regarding its use in animal feed do not always exist as it is only recent events which indicated the need to regulate for this substance. However, some countries have established regulations and do not permit the use of melamine in animal feed.” Indeed, the FAO specifically states: “Melamine is not permitted in food or feed stuffs.”
Nevertheless, the FAO says, melamine is often used in agricultural fertilisers. But, has also warned that the commonly used pesticide cyromazine can break down to form melamine (PDF document). This might also explain why melamine has been found in lettuce, water cress, tomatoes, mushrooms, potatoes and other agricultural products in China. Contamination levels are very low at 17 milligrams of melamine per kilogram of mushrooms, for instance. They are notably low compared to the levels of melamine found in contaminated infant formula milk, which were as high as 2560 milligrams per kilogram of ready-to-eat product. The levels of cyanuric acid in these products is unknown.
Sciencebase regular “Offy” pointed me to the North Korean publication The Daily NK, which asks whether there were melamine deaths in 2005. “According to merchants trading between China and North Korea, the Chinese Melamine-tainted milk affair started in Pyongyang in the summer of 2005. At the time, infants who ate imported Chinese powdered milk fell unconscious and, in more serious cases, died.” At the time, the North Korean authorities tested imported Chinese milk and banned it on the basis of their findings.
Because of the pet food problem, pet owners like Offy, have been following this stayed on this for well over a year. “Politics has trumped health in favour of industry for a very long time in the US…it’s not just a problem in China,” she says. Cai Jing blames a lack of supervision for the melamine crisis and suggests an approach that will allow China’s fledgling market economy to continue to grow but at the same time minimising the chances of a similar scandal occurring again. It says that the melamine milk crisis has taught China that government oversight to spot corruption is essential, but it also suggests that the government not be allowed to simply meddle with the market. This would, Cai Jing says, be the only way to ensure a safe food industry.
Please use the Share button to send this post to interested friends or colleagues or to add it to your Delicious, Digg, or Facebook account.
More melamine news
Posted: 07 Oct 2008 09:42 AM CDT
In case you ever wondered about that, the journal of clinical pathology investigates death by swallowing molten gold and if it results in bursting of the internal organs. For this purpose they poured molten lead into a bovine larynx and watched what happened:
"Based on these findings, we suggest that the development of steam with increasing pressure might result in both heat induced and mechanical damage to distal organs, possibly leading to over inflation and rupture of these organs. Direct thermal injury to the lungs may lead to instantaneous death, as a result of acute pulmonary dysfunction and shock, as shown by Brinkmann and Puschel.4 Even if this is not the case, the development of a "cast" (once the metal congeals again) would completely block the airways, thus suffocating the victim.
In conclusion, we have shown that in the execution method of pouring hot liquefied metals into the throat of a victim, death is probably mediated by the development of steam and consequent thermal injury to the airways."
Posted: 07 Oct 2008 09:00 AM CDT
One of the hot topics in evolutionary biology concerns the relative contributions of protein coding sequence changes and non-coding changes that lead to differences in the expression of protein coding genes. A subset of this debate can be summarized as cis versus trans. Non-coding sequences that regulate gene expression are known as cis regulatory elements (CREs). The protein coding genes that bind to CREs and control the expression of genes act in trans.
That's the background,and here are some more details. The poster boy for the importance of CREs is Sean Carroll, who argues that the pleiotropic effects of trans changes makes them unlikely to play a large role in the evolution of form (doi:10.1371/journal.pbio.0030245). On the other side of the debate is Jerry Coyne, who penned a strongly worded opinion piece with Hopi Hoekstra arguing that the evidence does not favor Carroll's hypothesis (doi:10.1111/j.1558-5646.2007.00105.x). The past few years have seen a multiple studies examining the relative contributions of cis and trans changes using analyses of gene expression in hybrids (e.g., doi:10.1038/nature02698). In the end, the data reveal that both cis and trans changes play important roles.
Along similar lines as the experiments testing for cis and trans contributions to gene expression differences, Bernardo Lemos and colleagues in Dan Hartl's lab have examined the dominance of cis and trans mutations by measuring gene expression in the parents and progeny of crosses between Drosophila melanogaster from various populations (doi:10.1073/pnas.0805160105). It's a nifty study, and I'm interested in a conclusion they draw regarding the temporal dynamics of cis and trans changes.Read the rest of this post... | Read the comments on this post...
Posted: 07 Oct 2008 08:00 AM CDT
Image via WikipediaVery interesting Semantic Web Gang from September, and a rather interesting panel I should add. It is no secret that I am a big believer in the Semantic Web and other “semantic” technologies although in varying degrees.
The page for the podcast seems to be down, but I will try and pen down some of the things that jumped out at me. It’s one of those things that you really have to think about when you’re building a platform business and who your target audience is.
IMO, it’s essentially impossible to build a consumer-facing business where your top selling point technology-based platform, and semantic companies are learning this harsh reality. In a B2B case, it’s possible to sell a platform, assuming it provides some compelling functionality and capabilities, but consumers don’t care about platforms, they care about functionality, so the trend of companies pushing capabilities and essentially “productizing” their platform is a trend that’s going to define “semantic” companies and hopefully that is one piece of marketing labeling that will die an early death.
But there is a third leg when it comes to the web. One of the best things Metaweb has done in recent months is to position Freebase as a data platform and not a destination site, or so it seems. In other words they have positioned themselves as a platform that can be leveraged by others to build those consumer facing products. I don’t know how they plan to monetize. Perhaps they will continue to do that with Freebase as a destination site (does anyone have an idea?). Similarly Calais is also targeting developers. On the other hand Twine is focusing in a different direction by making itself a destination site, which is not as compelling a proposition, especially since you don’t get the kind of quantum leap in functionality and productivity needed to switch over from your existing tools. Instead of becoming a destination site, it should suck in data and use the underlying infrastructure to help you find more relevant and interesting information. There are only so many interfaces one can use at any time, so I am not going to change my interface unless there is a really good reason to do so.
This is not a rant against Twine, which I do use (mostly via the daily digest, which should be a hint in itself), but rather one in flavor of the developer facing platform. We need to figure out how to monetize that model, a model that does not lend itself to advertising support, nor to the ability to generate tons of eyeballs, but to allow other people to build on top of their capabilities.
Posted: 07 Oct 2008 06:10 AM CDT
I’m running out of energy for political posts this election cycle and am on the verge of putting a moratorium on politics on A Free Man. But, I’ve had this one in the queue for some time and wanted to throw it out there before the ban. Today, I want to talk about science and politics. That’s right, boys and girls, a two-fer. Chris from Formerly Fun* sent me a link to the Scientists and Engineers for America’s comparison of the two major presidential candidates statements on issues of science, health care and technology. Inspired, I went through a number of interviews focusing on science and engineering that have been published with both candidates and picked out a few issues on which the candidates differ.
One of the things I found most remarkable was the similarities in the two candidates’ platforms when it comes to science and engineering. When it comes to important issues like embryonic stem cell research, climate change, scientific integrity and even alternative energy, there are little or no differences between the two candidates’ statements. There are little differences in numbers and approaches on things like offshore drilling, reduction of emissions and nuclear power, but these have been well covered by the media.
It’s important to keep in mind that what follows is what the candidates say in interviews to science publications. Now, it should be noted for those of you who were born yesterday that what a politician says and what a politician does are often entirely different things. It’s worth looking back in the past to see how each candidate has actually voted.
But let’s look at a few important differences on issues that aren’t being covered by the media. I’ve found three major science issues in which McCain and Obama have expressed notable disagreements. I’ve tried to be objective, but in the interest of full disclosure, I am an Obama supporter.
This is the type of science that often gets picked up on by politicians as wasteful of the government’s money. You’ve seen the headlines, millions of dollars spent to study grizzly bear DNA in Montana. The thing is, basic research drives most innovation in science and engineering. In general, drug companies don’t come up with the major breakthroughs in drug discovery, researchers in universities and publically funded institutes looking at things that seem trivial to the public at large make these discoveries. Drug companies fine tune them. The scientists that you’ve heard of - Einstein, Darwin, Mendel, Pasteur, Curie, Watson, and so on - we’re doing research that would have seemed as laughable to the layperson as studying the reproductive habits of blue crabs . Take home message, basic research is absolutely essential to scientific progress.
Obama has stated that federally funded basic research is one of his highest priorities in the science and engineering arena. He has pledged to double the basic research budget for engineering, mathematics and physical and life sciences over the next 10 years. McCain also has promised to fight for increases in funding for some scientific agencies. Crucially, however, he has promised a freeze in discretionary spending (which includes federal money for research) for one year.
OK, it’s becoming clear as I write this that I will not be able to be completely objective. For the last eight years, the Bush Administration has funded only abstinence-only sex education in the public schools. This has not worked. In 2006, the teenage pregnancy rate in the USA (already the highest in the industrialized world) rose for the first time in 14 years. Rates of syphilis and gonorrhea have risen steadily since 2000. McCain supports continuing this failed policy. Obama supports comprehensive sex education. This would include abstinence programs, but also would ensure that all taxpayer-funded federal programs are medically accurate and include information about contraception.
Evolution vs Creationism
Now, this is one of my biggest science and education issues. Both candidates are committed Christians and both candidates believe firmly in evolution. When asked if intelligent design (creationism) should be taught in the schools, McCain said in an interview with the Arizona Star that “all points of view” should be presented and “to say that we can only choose one line of thinking or one belief on how people and the world was created…there is nothing wrong with teaching different schools of thought.” Obama said in an interview with Nature, “I do not believe that it is helpful to our students to cloud discussions of science with non-scientific theories like intelligent design that are not subject to experimental scrutiny.” Read between the lines and I think you’ll discover the differences between the two candidates. McCain is OK with teaching creationism, Obama is not.
There are also some differences of opinion on things like NASA (Obama may cut funding), net neutrality (McCain proposes letting the market handle it, we know how well that works) and nuclear energy and offshore drilling. I’m trying to keep this post short and to the point. I report, you decide.**
* If you aren’t reading Chris’ blog then stop what you’re doing right now and go and read it. Ignore the scary pink theme and see what she’s got to say. Simply one of the best around, particularly when she writes about politics and society. And I’m not just saying that because we’ve arranged a marriage between her daughter and my son.
** Please don’t sue me Rupert.
This posting includes an audio/video/photo media file: Download Now
Posted: 07 Oct 2008 05:55 AM CDT
An article in last week’s Science caught my eye. In An International Plan to Hatch Scientist-Entrepreneurs, there’s news that a panel at the summer meeting of the World Economic Forum (WEF) announced plans to award five $10,000 seed grants to the most compelling joint R&D proposals arising from interactions at the meeting between scientists and business leaders.
The trouble with entepreneurship of this kind however, is that you have to be a lot smarter than me. Or at least someone who thinks they understand either business or product design better than I.
Okay, joking aside. There are a lot of useful resources out there for enterprising young scientists. Like this Resource for Scientist Entrepreneurs.
Check it out.
Posted: 07 Oct 2008 05:20 AM CDT
The Nobel Prize for Physics 2008 is announced here Tuesday, October 7.
The Nobel Prize in Physics goes to Yoichiro Nambu (born 1921) of the Enrico Fermi Institute, University of Chicago “for the discovery of the mechanism of spontaneous broken symmetry in subatomic physics” and to Makoto Kobayashi (b. 1944) of the High Energy Accelerator Research Organization (KEK) Tsukuba, Japan, and Toshihide Maskawa (b. 1940) of the Yukawa Institute for Theoretical Physics (YITP), Kyoto University Kyoto, “for the discovery of the origin of the broken symmetry which predicts the existence of at least three families of quarks in nature”. You can read the full press release from the Nobel org here.
As I mentioned in my previous post on the 2008 Nobel Prize for Medicine and Physiology item, yesterday, the team, led by Simon Frantz have been using modern web 2.0 type technologies, including RSS and twitter to get the word out to journalists as fast as they can. Part of the reason, apparently, was to save journalists from suffering serious F5 button finger strain at announcement time.
Anyway, here’s the twitter update page - Nobel tweets. They also created a neat little widget so that we could embed the timetable into a website (see left). As you can see, the 2008 Nobel Prize for Chemistry will be announced Wednesday October 8. I’m hoping once again for some straight chemistry, rather than bio-flavoured molecules, as this will give me a chance to get my teeth into my journalistic alma mater as it were.
Posted: 07 Oct 2008 05:15 AM CDT
Posted: 07 Oct 2008 02:23 AM CDT
At BiRC we have a small study group where we are reading Michael Lynch’s book, The Origins of Genome Architecture. We take turns presenting a chapter, and last time it was my turn and the chaper (chapter 3) is on the Human Genome.
Below are my notes. I’ve tried to translate basepairs and percentages into meters, ’cause it helps me visualise the relative sizes. Even though it still boggles my mind a bit that the human genome is about 2m if you stretch it out. Well, that can’t be helped. Three billion is a lot, even if it is three billion very tiny things…
The human genome
The human genome is about 3Gbp which is about 2m if you stretch it out. Of this, about 1%, or 2cm, is coding. That doesn’t mean that only 1% is genes, ’cause most of genes (even protein coding genes) are not actually coding. We’ll get to that later.
There is nothing unusual about the human genome. Not compared to other multicelular eukariotes, at least. It is not the largest or the smallest and it does not have an unual number of genes. In fact, it is common as mud.
The genes are grouped into families, where the families are phylgenetically related. Some people have argued that the number of genes in a family tells you something about the importance of the family, but the distribution of family sizes could just as easily be explained by a stochastic birth/death process, at least if the gene families have different birth/death ratios. (This begs the question of why they should have that, but the chapter doesn’t say and I don’t know).
Introns and exons
The protein coding genes consist of introns and exons. The exons are what is left after the transcript is spliced and the introns is what is thrown out.
A personal comment: remember that exon is not synonymous with coding. I’ve seen people confused about this (and made the mistake myself in a script or two). The coding sequence starts somewhere along the sequence of exons and stops somewhere before the exons end. The coding sequence is a sub-sequence of the exons.
Back to the chapter…
The average exon length is about 0.15kbp while the average intron length is about 4.66kbp. So introns are on average about 40 times as long as exons. If we imagine (not to scale this time) that the exons are 1 cm long, then we have 40 cm of introns between them.
That is a lot of intron…
Since complex organisms doesn’t seem to have dramatically more coding genes than simpler organisms, alternative splicing has been suggested to explain the complexity.
On average we have 2.6 different splice products per gene. As far as we know, there is less alternative splicing in C. elegans and D. melanogaster, but then we know a lot more about alternative splicing in humans and mice that we do in any other organism, so we are boundt to have seen more rare splice variants here and the extra splicing we are seeing might easily be a selection bias.
We don’t really know how much of the alternative splicing is functionally important and how much is random “noise”.
How much regulatory DNA do we have? Based on conserved regions in the genome (which is probably a very conservative estimate) we have a few percent of the genome.
It seems, however, that the fraction of the genome that is conserved increases with organism complexity, so perhaps complexity is all in regulation?
Everything and the kitchen sink seems to be transcribed, and most of it differentially expressed, but how much of this is spurious we do not know.
We do know about different non-coding RNA genes, such as miRNA. Although miRNA is only found in multi-cellular organisms, RNA interference is found in all domains of life.
Even accounting for regulatory DNA, 95% of the genome — 1.9 m — has no function that we know of. Know of being the key word here, of course. Don’t call it junk before you know that it is really doing nothing…
There are about 100 times as many mobile elements as there are coding genes, and 75% — 1.5 meter — of the genome is a product of some mobile element or other.
(I have a lot of notes about the different kinds, but quite frankly I find it a bit dull, so I am not going to mention it here…)
There are about half as many pseudogenes as coding genes.
There are various mechanisms for introducing pseudogenes in the genome, including re-insertion of cDNA, tandem duplications and just plain inactivation of a gene.
The first two cases are likely to introduce pseudogenes “dead on arrival”. A re-inserted cDNA won’t have the regulatory mechanisms to get transcribed, and a duplication is likely to disrupt it as well.
Pseudogenes seem to have a halflife of ~37MYA (halflife of the time it takes till we don’t recognize it as a copy of another gene) compared to a halflife of ~7.5MYA for active duplicated genes. This seems to indicate that there isn’t much selection working against dead-on-arrival genes compared to duplicating an active gene and thus potentially doubling its product.
The chapter closes with an analysis of the human lineage and our evolution. (Can we finally find something that makes us special?)
It seems that we have seen an increase in substitution rate on our line, but Lynch argues that what we are seeing is not so much adaptive selection but rather a reduced negative selection.
There can be different explanations for this. A reduced population size can have reduced the effects of selection. A change in behaviour could have changed our fitness landscape, so traits that would normally be selected strongly against changing are now free to vary.
Posted: 07 Oct 2008 02:00 AM CDT
The Personal Genome Project (PGP) was established to analyze and publicly share the genomes and personal information of up to 100,000 volunteers in order to advance understanding of “genetic and environmental contributions to human traits and to improve our ability to diagnose, treat, and prevent illness.” In the first phase of the PGP, ten volunteers (the “First 10″ - see information about the First 10 here on my blog and at the PGP website) have had their DNA analyzed and have given their personal information.
Last month, George Church, the PGP’s principal investigator, reported that the project expected to publish data about the First 10 on its website in mid- to late October. Church might have meant genotype (i.e. sequencing) information, since some information about phenotype, health history, and medication has already been posted on the PGP website. There is information about each of the 10 participants, although there is currently no active link to their genetic information:
Note that the First 10 are listed as “Participant #1″, “#2″, etc. I debated about whether or not to attempt to identify them based on sex, ancestry, and date of birth, but since it was so simple to do that I decided to assign a name to the Participant number (I’m pretty sure I got them all right, depending on the quality of the source information I was able to find online). Indeed, the PGP has clearly stated over and over that anonymity cannot be guaranteed for participants. Additionally, I’ve always felt that one of the goals of the first phase of the PGP was to educate people about the effects of making your genomic sequencing information and health information freely available online. Some would argue that the effects are completely or mostly dangerous, while others would argue that the effects are completely or mostly benign. The PGP might help examine some of these questions.
Posted: 07 Oct 2008 01:00 AM CDT
This article was published on Highlight HEALTH.
Other Articles You May Like
Posted: 07 Oct 2008 12:48 AM CDT
The last week I’ve been running scripts to analyse a whole genome alignment, and I got some weird results. In some parts of the alignment, I was seeing way too much sequence divergence than there should be.
Now, manually inspecting 2Gbp of alignment is not an option, so I wrote a program to plot various summaries of chunks of the alignment.
Still, it is a lot of alignment, so scanning the genome with the plots didn’t work either, although the plots clearly showed that something was wrong.
I’ve been scratching my head about this for a while, and it wasn’t until I was heading to bed yesterday that it hit me: parts of the sequences are repeat-masked, so the case varies in the alignment. I consider A != a so I am seeing more variation than is really there!
I feel so stupid now. If only I had taken a look at the actual sequences, this would have been obvious! But I didn’t, I wrote a program to summaries the data instead.
Stupid stupid stupid…
Posted: 06 Oct 2008 11:23 PM CDT
Posted: 06 Oct 2008 11:04 PM CDT
|You are subscribed to email updates from The DNA Network |
To stop receiving these emails, you may unsubscribe now.
|Email Delivery powered by FeedBurner|
|Inbox too full? Subscribe to the feed version of The DNA Network in a feed reader.|
|If you prefer to unsubscribe via postal mail, write to: The DNA Network, c/o FeedBurner, 20 W Kinzie, 9th Floor, Chicago IL USA 60610|