Posted: 29 Sep 2008 05:38 PM CDT
Todd Oakley, of UCSB and more importantly, the Evolutionary Novelty Blog, forwarded this to me. UCSB is looking for an Asst. Prof. in Evolutionary Genomics. If only they had said "Phylogneomics" then I would have written a longer posting ...
Posted: 29 Sep 2008 04:01 PM CDT
I recently tasted raw habanero chili pepper for the first time. Just to give you an idea they rate at about 200 000-300 000 scoville units, compared to say jalapeños which have a measly 4000. This means that you have to dilute them over 200 000 times in sweet water before they stop burning. Needless to say it wasn't a very good idea and I had a near-death experience as my airways swelled so much that I could no longer breathe for nearly a minute. Do not underestimate the danger of hot peppers, they can be lethal. I was surprised to learn that birds can eat said peppers without so much as a sweat. Apparently it is mostly effective against mammals, and birds are immune to capsaicin, which makes for a clever way to get the damn squirrels out of your bird feeder. All of this is simply a segway to introduce another beer-fueled science debate we had at the pub. Is pain sensation limited to mammals? Warm blooded organisms? vertebrates?
You might recall that a while back a (very poorly conceived) paper about fish feeling pain created quite a stir. I suppose it all comes down to your definition of pain. For something we feel so ubiquitously pain's definition is rather elusive. Is it the "discomfort" you feel to a noxious stimulus, is it a reflex as a result of injury, is it the emotional suffering translated by our higher brain centers in response to the stimulus? As somebody who's worked with both fish and rodents I'd be inclined to think that all vertebrates feel pain. In fact by watching how slugs react to a poke, I think they might even be able to feel the essence of it. How else would they have survived this long if they couldn't learn from injuries to stay out of harm's way?
here is what the Wellcome Trust has to say about the subject:
"Nociceptive nerves, which preferentially detect injury-causing stimuli, have been identified in a variety of animals, including invertebrates. Indeed, the leech and sea slug are classic model systems for studying nociception. However, it is believed that invertebrates are capable only of stimulus-response reactions and lack the necessary brain system that vertebrates have to process pain.
In vertebrates, nociceptive information is collated and augmented in the brain and signals are relayed down the nervous system to alter the intensity of pain. All vertebrates possess the primitive areas of the brain to process nociceptive information, namely the medulla, thalamus and limbic system.
However, one area of great importance for pain perception in humans is the cortex and its relative size decreases as we descend the evolutionary tree. For instance, in relative terms, the cortex gets smaller going from humans, through primates, mammals, birds, reptiles, amphibia and finally to fish, which possess only a rudimentary cortex."
Posted: 29 Sep 2008 03:38 PM CDT
I recently blogged about Barbara Wagner who was told by the Oregon State Health Plan that they would pay for assisted suicide but not for the chemotherapy her doctor recommends. Anyone who has followed assisted suicide around the world knows this is one of the many consequences of offering death instead of care and compassion.
Why do I think this is relevant on a blog about biotechnology? Interestingly, it was the big-bad-for-profit-biotech company Genentech that offered Barbara the drugs for free. It was the government-run health insurance that told Barbara that they would pay for her to die and not for her to live.
Washington State will vote this November on I-1000, an initiative, like the one in Oregon, that would allow physicians to write a lethal prescription for terminally ill patients. It's supporters say is about compassion and choice for those who suffer from a terminal illness. Look closer and one sees that it is the insurance companies that will have the "choice" to offer the much cheaper assisted suicide instead of the more expensive medical treatment and pain control. Those who are the least able to pay, will be the most effected.
Martin Sheen, who everyone knows is no conservative talking head, agrees. From the NO on I-1000 website:
You can hear his radio ad here.
For those of you who live in Washington state take notice. If you want your insurance plan to write you a letter like the one Barbara received when you have a terminal illness, then vote for I-1000. If you would rather have your insurance pay for the expensive doctor-recommended treatment instead of the cheap over-dose that will kill you early, then vote NO on I-1000.
Posted: 29 Sep 2008 02:02 PM CDT
This First Annual Conference for New Jersey Biotechnology Educators will be held on Saturday, Oct. 4th at Monmouth University in West Long Branch, New Jersey.
I'm excited about attending this conference, not only because of the biotechnology part, but because I've reading Sarah Vowel's book Assassination vacation and I'm looking forward to seeing the last resting place of President James Garfield. Sarah Vowel is an incredibly funny commentator on NPR's "This American Life" and so, even though I don't usually read about people making pilgrimages to famous presidential sites, I had to read this book.
What can you look forward to seeing if you come to West Long Branch?Read the rest of this post... | Read the comments on this post...
Posted: 29 Sep 2008 01:17 PM CDT
The September 20th issue of Science had a news article that I hope Bitesize Bio readers didn’t miss. In case you do however, the article was And Then There Was One:
The attitudes and ethics of those 26 former Yale students are also portrayed - a PhD creates as many career problems as they solve, with the successful researcher “doing whatever it takes,” and at times, learning from some tough choices. Check it out.
Posted: 29 Sep 2008 11:12 AM CDT
I was reminded of this New York Times interview with James Thomson by a reader of this blog. (Thanks Brian!) James Thomson was one of the first scientists to take an IVF embryo and extract stem cells.
I have always been impressed with Dr. Thomson. I know he destroyed human embryos in his research, but he has never trivialized it. He has always been very clear that destroying human embryos was a significant moral issue. Unlike many in the scientific community, he does not describe a human embryo as nothing more than just some amorphous ball of cells. He said in the 2007 interview:
In fact, Thomson was so concerned about the ethical implications that he consulted two ethicists before starting his work with human embryos:
The main point I want to drive home is this: In this age where society thinks science has all the answers, we need to remember that while science has improved our lives immensely, it will not continue to do so without proper ethical oversight. We have a right, no matter what our education or occupation, to say where we want our tax dollars to go and want kind of research we want to go on in our institutions of higher learning. We cannot give researchers carte blanche to play with human lives, no matter how immature, in the name of scientific advancement. To do so means we "have not thought about it enough."
Posted: 29 Sep 2008 10:50 AM CDT
I have just received my September print copy of Biophotonics International, a monthly magazine that would collect "photonic solution for Biotechnology and Medecine". I usually skim it in order to find some news about my well-beloved reporter genes.
I forget to mention that I got my FREE subscription to Biophotonics International (and other interesting magazines) at http://reportergene.tradepub.com You can try to apply for your own free subscriptions, and so giving a little help to Reportergene (strongly suggested: it works).
Posted: 29 Sep 2008 10:46 AM CDT
Induced pluripotent stem cells (iPS) are the new alternative to embryonic stem cells. They behave like embryonic stem cells, but they are created from adult cells, side-stepping the moral trespass of ripping open a human embryo.
The problem with iPS cells was that to induce pluripotency (the flexibility to become many different types of cells) researchers had to use retroviruses that would insert transforming genes into genetic material of the cell. These retroviruses have been known to cause cancer.
Last week scientists announced that they induced pluripotency with adenoviruses, which are considered to be harmless because they do not insert the transforming genes into the DNA of the adult cell. From the Washinton Post:
Scientists last year shook up the scientific and political landscape by discovering how to manipulate the genes of adult cells to convert them into the equivalent of embryonic cells -- entities dubbed "induced pluripotent stem cells," or iPS cells -- which could then be transformed into any type of cell in the body. Subsequent work has found that the cells can alleviate symptoms of Parkinson's disease and sickle cell anemia in mice.
Posted: 29 Sep 2008 10:43 AM CDT
Of all the direct-to-consumer genetic tests currently available to the public, early gender DNA tests are among the most controversial. The test allows pregnant women to submit finger prick blood samples which the lab screens for the presence of Y-chromosomal DNA from the fetus; Y-chromosomal DNA positive indicates a boy, negative indicates a girl.
Karen Kaplan of the LA Times looked into the accuracy of gender DNA test kits in February of this year. And a lively discussion among Eye on DNA readers follows my post: Is the Pink or Blue early baby gender DNA test accurate? One of the commenters is Terry Carmichael, VP of Marketing & Sales at Consumer Genetics, manufacturer of The Pink or Blue Early DNA Gender Test.
Terry is the founder of Gene Tree DNA Testing Center which was sold to Sorenson Genomics in 2001. He also helped launch at-home DNA paternity DNA tests in major U.S. drugstores in 2007 (see previous Eye on DNA post). I was impressed with Terry’s openness and invited him for an email interview.
Hsien: What is your company’s motivation for providing an early gender DNA test direct to consumers?
Terry: Trying to predict the sex of a baby has been a centuries old game within families. Families want to know the sex of a baby for many reasons. Most want to make an announcement at a family gathering, or surprise their husband with the anticipated gender, or preparing siblings for a new baby boy or girl. Others want to know so that they can prepare siblings that will have to share rooms, or to begin to decorate a room for the baby based on gender. The main motivation for Consumer Genetics is the gratification we get when helping families plan for the future by offering them the information they are seeking to know.
Hsien: Can you tell us more about the quality assurance protocol for the Pink or Blue DNA Gender Test?
Terry: The Pink or Blue test is based on several large scale studies that have scientifically proven the ability to determine gender by detecting Y-chromosomal DNA of fetal origin in a large sample of a mother’s blood (10 ml). The accuracy of this method in a clinical setting has been shown to be between 97.8 to 100% within a population of 1,837 pregnant women. The Pink or Blue test uses the same molecular technique as in the studies (Polymerase Chain Reaction) along with a proprietary method of purifying and amplifying the baby’s Y chromosomal DNA within a much smaller sample of the mother’s blood (usually 60-120 microliters). The company looks for data from the DNA test that shows the baby is a boy. If this data does not show this, then this suggests that the baby is a girl. There are times when the data is not clearly one or the other - imagine a few data points that are on either side of a line. In this case, we report the test as inconclusive. Due to this complex "signal-to-noise" issue, we regularly run at least 2 tests for each sample to increase the probability of a conclusive result. If all tests are "inconclusive," we then ask the customer for a new sample. Therefore, just like ultrasound, we have a portion of samples that we cannot determine gender from, and we have the customer send a new sample for re-testing. This second sample will nearly always give us a conclusive result.
Our laboratory has a documented quality assurance system in place to ensure the proper functioning of all equipment and reagents. All new reagents are thoroughly tested before entering the production line. We also purify a control sample along side a batch of real samples to ensure that there is no reagent failure or laboratory-caused contamination. About 33% of all the sample wells in a PCR reaction are controls, ensuring that all reagents are working properly. For each portion of a sample that is tested, the Pink or Blue DNA Gender Test laboratory procedure is run in triplicate. So, for a standard sample, where 2 portions are tested, there are actually 6 data points showing boy or girl, 10 data points with unique controls for that specific sample, and dozens of controls indicating that all reagents were working properly.
The lab documents all this activity and is working towards ISO and CLIA accreditation. Although accreditations are not currently needed for gender testing due to it is not used for medical or diagnostic purposes, the company recognizes that accreditation will add more creditability, and as more regulatory guidelines are expected in the future, it makes good business sense to have a strong, accredited quality system in place.
Hsien: What factors can contribute to inaccurate results? How can consumers ensure the most accurate results possible?
Terry: It is very important that our instructions are carefully followed. The DNA preservation cards must be completely filled with the appropriate amount of blood in all three specimen blotting areas of the card. The quantity of a baby’s DNA in the mother’s blood is very minute. Therefore, the more blood, the more fetal DNA; and the higher the chances are for a conclusive result. It is also important to collect the sample no earlier than 7 weeks, post-conception. Specimens collected earlier than this eligibility date may not have enough fetal DNA circulating in the blood for our DNA test to detect. Contamination of the sample with male DNA from outside the womb can also occur. We have a proprietary method that detects this kind of external contamination, but once contamination is confirmed we cannot provide accurate results and a new specimen is needs to be sent in. The best way to ensure the most accurate results is to follow our instructions, watch our instructional video, keep away from males while providing the sample, collect the proper amount of blood, and make sure that the area used for specimen collection is clean.
Hsien: Why do you think people are so eager to know the sex of their baby before delivery?
Terry: That is a complicated question and one that is highly specific to each individual. We do not survey our clients' intentions, but many volunteer their reasons for DNA testing. Most commonly these are to make an announcement at a family gathering, surprise their husband with the anticipated gender, preparing siblings for a new baby boy or girl, and many women are simply excited and anxious about their pregnancy and want to know their baby's gender as early as possible. They just can't wait to find out.
Hsien: How would you respond to critics of early gender detection who say that the various methods, including DNA tests and ultrasound, are being used for sex selection?
Terry: There are several companies providing products to select gender, and gender selection is legal in the United States. Check out places like Amazon.com, where gender selection kits are for sale.
However, this is not what we are all about, here. We are about helping people who are excited and want to make an announcement at a family gathering, or surprise their husband with the anticipated gender, or preparing siblings for a new baby boy or girl, or just to help a mother-to-be who is thrilled about her pregnancy and wants to know her baby's gender as soon as she can.
Our DNA test are not be used for gender selection and our consent for states this. People using our gender testing service have consented not to use it for gender selection purposes. We are clear about this, and we will continue to refuse to provide our services for those means. To further assure this position we regularly turn people away trying to purchase from China and India, where gender selection procedures are of great demand.
Posted: 29 Sep 2008 09:57 AM CDT
I love the Boost library. It is without a doubt one of the most important libraries for C++ development. I use it in practically every program I write.
Right now, I’m working on a Mac, and I wanted to use Xcode for my programming. Sounds reasonable, really. It is the Apple tool for it, and since it uses the GCC tools under the hood, I am familiar with error messages and such, so it should be straightforward to use.
I find it practically impossible to link with Boost.
I’ve installed Boost using the “port” tool, so it is installed the way it would be on e.g. a Linux machine. That means that the header files are found in /usr/local/include and the libraries in /usr/local/lib.
Setting the path to the header files in Xcode isn’t so much of a problem, but getting it to link with the right library is beyond me.
As far as I’ve figured out, you need to add the right .a file. Doing this is not so easy, ’cause the GUI won’t let you find /usr/ unless you do a bit of magic to unhide that directory. If you manage to add the library, at least this is how it works for me, you can build the Release but not the Debug target, and even though you added a .a file, it will link with the corresponding .dynlib file, so you cannot distribute the compiled file without requireing people to have Boost installed.
How does it suck? Let me count the ways…
Posted: 29 Sep 2008 09:45 AM CDT
I know others have written about this already but I had to add this to my collection of Science Faux Pas because it is pretty good. Nature had a recent issue that was covering the US election. And look at the front and back cover ... they claim it was an accident but hard to imagine given the posing/color matching. I note I first heard about this from Bora on FriendFeed. And now the Times Online has a whole story on it.
Posted: 29 Sep 2008 09:00 AM CDT
Great presentation by Carole Goble that I found via Richard Akerman. In the presentation, Carole hits upon many of my favorite themes including data driven research, the importance of open data, etc.
I will point to slide 24 that really drives home a point that most people do not talk about enough; Methods are scientific commodities. From the beginning of publication, we have had a “methods” section in our papers. So why hasn’t electronically capturing our workflows, and making them available in some common format, become the norm? This could be done via depositing the workflows at a place like OpenWetWare, and computational workflows in a place like MyExperiment. Yes, there are cases when your workflow is somewhat novel, but you are unlikely to publish that anyway, so it’s a somewhat mooth point
The Future of Research (Science and Technology)
Posted: 29 Sep 2008 08:41 AM CDT
A new season of the bayblab podcast is back (rss, mp3). As usual we drunkenly ramble about the cancer carnival and specualte on how dogs can smell cancer, we talk about the different classes of substances abused in sports and why it is unethical, we talk about personal genetic information, privacy and companies like 23 and me, and finally we display our ignorance by tackling basic science questions....
Posted: 29 Sep 2008 08:00 AM CDT
Calling all scientists and science-fans: you can help with science education by letting students know you're interested. How? Go and comment on classroom blogs and wikis.
I've been gradually collecting some blogs from different classes and I've even had some brave volunteers offer theirs for review.
So here goes:Read the rest of this post... | Read the comments on this post...
Posted: 29 Sep 2008 04:00 AM CDT
Dairy farmers have been feeling the squeeze for years, particularly in parts of the world where technological advancement has been slow in coming and so their profit margins on their milk output have not been lifted by improved efficiency. In order to boost profits milk has been diluted. However, this brings with it the problem of falling quality - dilute with water and measurable concentrations of milk proteins, fats, and sugars fall. Dilution by up to 30% has not been uncommon, which is where melamine (as I’ve mentioned) comes in. Melamine is a small organic molecule with a high nitrogen content that can easily fool the quality control equipment into thinking that nitrogen (from protein) is present at normal levels and so the milk is passed as good.
Unfortunately, it is possible thatmelamine accumulates in the body and causes toxicity problems - basically damaging the kidneys and forming stones (solid deposits within the kidneys or bladder). Infants fed regularly with milk containing melamine will be particularly susceptible to these effects. As we have seen tens of thousands have been affected and several have died in China. Why this problem is not more widespread, given the rather large number of infants potentially having been drinking contaminated formula-milk for months is unclear.
Hsieh Teh-sheng, director of the Taiwan Urological Association and chief of Cathay General Hospital's Department of Urology told the Taipei Times, that while there is no direct toxicity information on melamine’s health effects on people, the level of melamine found in the milk products is “not particularly high”. He says that kidney stones or other effects blamed on the melamine “could just as easily be caused by other harmful chemicals,” which is a point I discussed in the original post.
However, cyanuric acid is often present in melamine samples and the two can react together to form crystals of uric acid, which can form stones. The current scandal could, whatever the final outcome, provide researchers with useful data on melamine toxicity. That said, if someone were drinking lots of coffee with powdered milk and does not have a lot of fresh water in their diet, this in itself is a risk factor for kidney stones regardless of any contaminants.
Sources in China have now said that Sanlu, which is at the heart of the controversy, was aware that its products were contaminated with melamine as long ago as December 2007. Fonterra, the New Zealand dairy company and 43% stakeholder in Sanlu claims to have approached the Chinese authorities as soon as it heard about the problem but was held back from going public because of the imminent Beijing Olympic Games. One can imagine there were additional pressures that prevented Fonterra from pushing for a solution. But, it cannot blame Chinese regulations for it failing to warn consumers as soon as it knew about the contamination.
Products across the globe containing milk imported from China seem to have been affected and authorities from Australasia and Asia to Europe and the US are withdrawing formula milk, coffee and tea drinks, candies, soup, cheese powder, biscuits, ready-made desserts, and chocolate. however, there are calls from some commentators that the US Food and Drug Administration (FDA) should be more forthright on its recommendations for consumers concerned with the melamine in milk scandal.
For those thinking of testing the products in their store cupboard, there’s a Craigslist item for sale here. It’s described as a “Rapid Melamine test kit—AgraQuant Melamine ELISA test kit”.
But, before you grab your credit card, think carefully whether you’d like to make ELISA (Enzyme-Linked ImmunoSorbent Assay) your friend. It’s a tricky test and probably not one you could rattle off in an afternoon with at least some biomedical background. Also, there’d be no point in testing your Ikea furniture for melamine, the “Melamine” they use is a polymer resin (a plastic, in other words) made from the small organic molecule melamine and formaldehyde, and no there’s no need to worry about using melamine cooking utensils or eating off a melamine-coated kitchen table.
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Posted: 29 Sep 2008 02:00 AM CDT
Last week, Randy Seaver of Genea-Musings posed a genetic genealogy question on his blog. I posted a possible solution in the comments there, but I am asked this question regularly and thought I would discuss it here.
At a recent meeting that Randy attended, a woman in the audience asked the speaker:
“I don’t know who my father is. He and my mother had relations in Naples, Italy back in the 1950’s and I was born. I have no siblings. My mother did not tell me his name and there is no father’s name on my birth certificate. Can DNA research help me?”
This particular situation is exceptionally challenging. If the child had been a boy, he would have his father’s Y-DNA and a decent chance at identifying his father’s surname (and thus could perhaps further elucidate his actual identity with the combination of DNA research and traditional genealogical research). If the unknown parent had been the mother, the daughter would possess the unknown parent’s mtDNA and a remote but possible chance of finding an mtDNA match and using traditional genealogical techniques to identify the mother.
Given this situation, Randy asked:
I agree that AS OF TODAY, there is little to no hope that the woman will discover the identity of her father. However, people almost always believe that this mystery will never be resolved because there is no Y-DNA or mtDNA solution. Of course, as we all know, the child inherited 50% of her genome from her father. It is my hypothesis that somewhere in that DNA is a clue to her father's ancestry which can ultimately be used to identify her father.
How will autosomal (non-sex chromosome) DNA reveal her father's identity? As genomic sequencing becomes cheaper and cheaper, it will be possible to sequence an entire genome relatively cheap (first under $1,000, then eventually under $100). With this technology, genealogical and medical organizations will use vast autosomal DNA and family chart databases to trace genes and mutations through genealogies. SMGF, for example, is already collecting both DNA and family charts, and is set to release the Sorenson Autosomal Database in the near future.
Additionally, earlier this year a deadly mutation that leads to colon cancer was traced to an English couple that emigrated to the United States in 1630, almost 400 years ago. Although not everyone with this mutation is descended from this couple, many are; thus, if you have the mutation, it is very possible that you are descended from this couple and this would provide a clue to your ancestry that could be explored with traditional genealogical research. With cheap sequencing scientists and genealogists will be able to trace unimportant 'quiet' mutations through time and genealogies, just as scientists have already done with health-related mutations.
So how will all this help the woman identify her father? Someday in the very near future she will be able to query her genome against a database of genomes and ancestries. Just as a deadly colon cancer mutation can be linked to a certain family, it is likely that the woman has one or more random mutations in her genome that are linked to certain families. Using traditional genealogical research (to rule out inheritance of those mutations through her mother, for example) and genetic technology, she might be able to use that knowledge to identify possible sources of half her DNA.
The scenario I posit requires two things which are not currently available:
For most people, being able to identify your own ancestors based on your own DNA poses few if any ethical dilemmas. However, what if your neighbor or your stalker or even law enforcement wants to use a sample of your DNA to identify your ancestors? Additionally, what if your living ancestor doesn’t wish to be identified? Does the ancestor have that right, or is possible identification through genetic genealogy just one of the consequences of parenting a child anonymously or simply having sex with another person?
Posted: 28 Sep 2008 08:33 PM CDT
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