Friday, October 31, 2008

The DNA Network

The DNA Network

happy hallowe'en! [the skeptical alchemist]

Posted: 31 Oct 2008 06:49 PM CDT

What are you up to today? I am not much of a carver, but if somebody is still thinking of what to put on their pumpkin, I think I have an idea for you: how about... the Black Man?





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Tales from the lab: the finale [Discovering Biology in a Digital World]

Posted: 31 Oct 2008 04:20 PM CDT

What strange things happen in the lab on Halloween? Read part I and part II to find out what's going on. (Reposted in honor of Halloween)

"All those beauties in solid motion All those beauties, gonna swallow you up

Hi hi hi hi hi hi
One time too many
Too far to go
I - we come to take you home"

- Swamp by the Talking Heads

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Evolutionary perspective on the genetics of osteoporosis [Yann Klimentidis' Weblog]

Posted: 31 Oct 2008 01:43 PM CDT

This review paper in Human Genetics discusses osteoporosis from an evolutionary and genetic perspective, and sometimes reads like a list of personal health guidelines (which is ok, I guess). I'm usually pretty reserved when it comes to criticizing papers on my blog, but I'm going to make an exception and say that this paper was somewhat disappointing, especially given that it was published in a high level journal: Human Genetics.
Ok, so first the obligatory point about how we are "stone age bodies living in a novel, modern world":
" ... current demographic trends will have the effect of altering what was once a positive adaptation for distinctive human bipedality into a serious set of "collateral" pathology among the modern elderly (Latimer 2005)."
...then a brief mention on the source of population differences: (I don't like the "Africans" generalization)
"Therefore, Africans more frequently have lactose intolerance, probably because they do not need as much vitamin D and calcium to maintain their (relatively strong) skeletons. On the contrary, skin depigmentation and high consumption of dairy products do not seem to protect Northern Europeans from fractures."
They also go on to explain the mechanism by which consumption of whole grain and milk products likely aggravates the risk of osteoporosis, which is pretty interesting.

He then briefly moves on to the genetics of osteoporosis with this statement which I find a bit hard to swallow, maybe just because I'm a too much of a hard-core adaptationist:
"It seems accurate to assume that if osteoporosis has a genetic determinant, its genetics will share peculiarity with the aging per se, being an example of "post-reproductive" genetics (Capri et al. 2008), which is difficult to explain by a selection process."
He argues that there would have been no selection against osteoporotic phenotypes since these cause problems later in life and would have no effect early in life, an argument which leaves me unconvinced:
"Therefore, children with a "pro-osteoporotic" bone architecture and lower bone mineralization were not selected against—which means, they were able to transfer their genes further on."
At the end of the paper are statements about the future of evolution in humans (which generally make me cringe):
"Is natural selection still a driving force in humans, given that our survival is often less dependent on genes than on technology?"
Osteoporosis: an evolutionary perspective
David Karasik
Human Genetics early online
Abstract: Increased life expectancy has led to an overall aging of the population and greater numbers of elderly people. Therefore, the number of people with osteoporosis has increased substantially, accompanied with an epidemic of hip fractures. Osteoporosis is an age-related systemic condition that naturally occurs, among mammals, only in humans. Osteoporosis is known to be highly heritable. However, assuming a genetic determinant for this post-reproductive disease to be transmitted from one generation to the next is counter-intuitive, based on the principles of human evolution, I will attempt to provide an explanation of the phenomenon from the point of view of evolution, selection, and changed environment in humans, which contributed to human longevity, while on other hand, contribute to diseases of civilization, including osteoporosis. There is a need to delve into evolution of human species in search for adaptive patterns to a specific environment that humans are operating in the last couple of millennia, to clarify whether "good" and "bad" genes exist, and how to find and correct them. The answer to the above questions will help us to identify causes of the current epidemic of osteoporosis and to pin-point a tailored treatment.

Health 2.0 Conference: Video Interviews [ScienceRoll]

Posted: 31 Oct 2008 01:21 PM CDT

Genome Technology Runs the Table on Open Access ... [The Tree of Life]

Posted: 31 Oct 2008 01:14 PM CDT

Wow.  Again, wow.  Genome Technology Magazine has dedicated in essence an entire issue to Open Access and they have a whole series on interesting things to say about it.  In addition they are making the issue available under a Creative Commons License so everyone can check it out.  Among the articles are:

Health Tweeple to Follow [ScienceRoll]

Posted: 31 Oct 2008 01:09 PM CDT


First, the word of the month award goes to tweeple (people on Twitter, the microblogger service).

Second, Mark Hawker made a list of the top 30 health twitterers to follow on his tumblr blog (screenshot below). He later wrote a post about other interesting health twitterers as well.

Twitter creates an easy way to get answers rapidly and make contacts easily. There is a huge health/medicine 2.0 community there.

Add me to your contacts on Twitter and let’s discuss the future of health.

      

Best Invention in 2008: 23andMe or Hype? [ScienceRoll]

Posted: 31 Oct 2008 12:50 PM CDT


TIME magazine published the complete list of the top 50 best inventions of 2008. The winner is 23andMe, the Google sponsored genetic company that provides SNP genotyping. Spittoon, the official blog of 23andme also covered the subject. While I think their service is important, Medgadget shared some major points with us and I must say they were right. These are the truest words I’ve ever read about direct-to-consumer genetic testing.

We say, TIME was probably sucking up to people whose lives have become a never ending effort to hype things onto the common man. You see, whether you take 23andme’s Anne Wojcicki and her husband Sergei Brin (co-founder of a website Google.com, an advertising agency with no customer service), or 23andme’s investor movie mogul Harvey Weinstein, or Navigenic’s venture capitalist John Doerr, they feel that they are changing the world. But really, considering the hype, aren’t they more interested in making money and elevating themselves to the level of revolutionaries, than furthering medicine and its technology?

Other interesting inventions:

      

Three lessons learned from Dr. Cox’s lecture on how to conduct a successful GWAS [Retail Genomics: The Science and Business of Consumer Genomics & Consumer Bioinformatics]

Posted: 31 Oct 2008 11:01 AM CDT

The genome-wide association study (GWAS) is an increasingly popular approach for identifying genetic factors influencing common, complex diseases. It also established the scientific basis of many consumer genomics tests. I am doing a live blog at the Consumer Genomics Workshop at Northwestern University.

  • Maximizing the power of GWAS

To maximize the power of a GWAS study, various approaches have been proposed.

According to Dr. Cox, staged-design (for example, 300 samples of 100,000 SNPs at stage I and 2,000 samples of 1,000 SNPs at stage II) is less popular now, because of the lower cost of genotyping nowadays.

Instead, it is more popular to utilize a public database of controls, which can significantly increase the power of the association study and decrease the overall project cost. An example of such a control database is Ilumina's iControlDB.


  • QC of the allele calling is critical

Bad samples can bias the genotype calling, which results in superficially results with very high apparent significance (thousands significant SNPs after FDR), as evidenced by the Q-Q plot.

Many allele-calling algorithms are based on the clustering of the fluorescent intensities. As such, bad samples (outliers) can cause confusing and wrong assignment by the algorithms.

I used to think that with thousands of samples involved, a couple of (even dozens of) bad samples should not be a big concern (i.e., the robustness of statistical modeling!), but I am wrong according to Dr. Cox.

  • Experiment design

Dr. Cox mentioned that the batch/plate artifacts have been observed in multiple studies. For instance, some of the plates containing only case and some of the plates containing only controls. This fact reminds me of statistical experiment design. We learned the same lesson in SELDI-TOF proteomics and microarrays.

Such a batch/plate effect can be tested by looking at the allele frequency of each plate: if you see dramatic different results from a plate, it suggest further investigation.


Nancy J. Cox, PhD is a professor of medicine and human genetics and chief of the Section of Genetic Medicine at The University of Chicago. Her research program is focused on development of methods to identify and characterize the genetic component to common, complex diseases and related traits. Diseases currently under study in the Cox computational lab include focuses on diabetes and diabetic complications, asthma and related traits, stuttering, specific language impairment, mesothelioma, breast cancer, Tourette Syndrome and autism. Her development of methods for genome-wide association studies has provided new insights into the genetic component of common human diseases.

deCODEme customer support has your answers [deCODE You]

Posted: 31 Oct 2008 10:07 AM CDT

deCODE Customer Rep Larus Jon Gudmundsson and Genetic Councelor Kristleifur Kristinsson

deCODE customer rep Larus Jon Gudmundsson and genetic counselor Kris Kristjansson MD

Tapping the vast resources of deCODEme scientists

The users of deCODEme show great interest in their results and are not afraid to ask questions. deCODEme customer support welcomes all questions and inquiries and taps the vast knowledge base and resources of its research teams to respond to all emails as comprehensively and quickly as possible. Among the more general questions we receive is the following.

Question
“I’m seriously thinking about doing the DNA test. Now I only have to decide from which company. How does your test compare with tests from other companies?”

Response
There are a few key differences between the services of deCODEme and its competitors.
deCODEme is provided by a company called deCODE genetics. Scientists at deCODE genetics have been carrying out research on human genetics for over a decade and have already produced a very large portion of validated discoveries of variations in the human genome that confer risk for common diseases. Our mission at deCODE genetics is to use genetics to help people to improve their health, and one of the ways we do that is by offering the deCODEme service. The same scientists, statisticians and geneticists who actually discovered the genes engaged in making that information useful to the public. At the same time they are continue to publish the results in the best scientific journals and have been doing so many years. Now, additionally, they simultaneously make those articles available on the deCODEme customer’s profiles.

However, it is also important to note that not only do we use our own internal expertise to develop our products, process your sample and analyze the resulting data , but we also give you direct access to this expertise, should you have any clinical or scientific questions. Our clinical support team includes an MD medical geneticist and genetic counselors that you will have access to at no extra cost. In contrast, most other companies offering DNA analysis are only acting middle-men and have to outsource much of the sample processing.

Another key difference is that the deCODEme analysis consists of information on 1 million markers, while our can only offer less than two thirds of that total. This means that if you have a deCODEme profile we can provide you with higher coverage now and significantly higher quality analysis of future research findings as we make new discoveries.

Our strategy is to offer a product that is as good and as useful as possible, which is how we provide real and long-term value to deCODEme customers. We have posted an entry on this subject on our blog.

The results are presented in a simple and clear format.
deCODEme provides a report on your sample on the www.decodeme.com website that you can unlock with your password. The report will contain your actual genotypes for the SNPs in question. Additionally, you will be provided with the raw data of the complete scan, i.e. about 1 million SNP genotypes. Reference to published scientific findings relevant to your results are also a part of the report, and are individually linked to each marker that is analyzed.

The report contains a disclaimer that although a SNP is individually associated with disease risk in deCODE´s own population studies, deCODE cannot predict how that SNP will interact with variants at other SNPs in any particular person.

There is a Site Tour available now on the website under “What is deCODEme” on our website. In addition there is a FAQ (frequently asked questions) section on the website.

The deCODEme browser.
We have recently introduced the deCODEme Genome Browser, a highly sophisticated on-site tool that enables to explore your results in detail. The Genome Browser is accessible on on the deCODEme website.

Best regards,

deCODEme customer support.

Tales from the lab, part II [Discovering Biology in a Digital World]

Posted: 31 Oct 2008 10:01 AM CDT

Strange things happen when it's Halloween week in the lab.

(reposted in honor of Halloween)

Catch up on the story by reading part I.

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Genetic testing for career advice [Genetic Future]

Posted: 31 Oct 2008 08:35 AM CDT

Note: I'm splitting this off from my earlier post on 23andMe's encouragement of genetic testing of children, since I think this rather speculative argument distracts from the main point of that post.

I mentioned in my previous post that there's a real danger that parents might try to use information from current genetic tests to steer their children in specific directions (and that at least one company is already touting such a test) - but the information available right now from genome scans simply isn't accurate enough to justify such decisions.

For instance, to mention a field close to my own heart, the genes currently known to affect athletic performance likely explain less than 5% of the variation in traits such as muscle strength and cardiorespiratory fitness. Any parent seeking to decide which sport their child would be best suited to would be far better off simply encouraging them to try a whole variety of activities and seeing which ones they were best at (and which ones they enjoyed the most); the addition of currently available genetic data would have marginal benefit, if any.

The same applies to an even greater extent when it comes to traits affecting career decisions - intelligence, personality, even attractiveness. Some of these traits are strongly influenced by genetics, but the actual genetic variants affecting them are currently almost completely unknown, and you should be extremely wary of anyone who tells you otherwise (e.g. these guys).

However, it won't be long before many of the genes underlying many traits relevant to career choices and life success are known, after which the equation is forever changed. Although in the vast majority of cases genetic predictions will still be probabilistic rather than deterministic (since there are many non-genetic factors that affect these traits) it would seem rational to gently steer children towards life paths that are most likely to maximise their overall potential, as determined by both genetic and non-genetic tests.

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Around the Blogs [Bitesize Bio]

Posted: 31 Oct 2008 05:30 AM CDT

Six highlights from “Around the Blogs”:

Help High School Kids do Genetic Engineering and Make Glowing Bacteria
“Why should professional scientists have all the fun?” Sandra shares stories of cool stuff in the classroom.

Talking Points for NIH Funded Science
Drug Monkey has some suggestions for scientists venturing into politics, amid the height of the US elections.

deCODE: The “Decide to Take Action” Line is Magic, is not Medicine
Drew Yates takes down the publicity approach of a personal genomics company - overhype unsupported genomic information.

An Eye-Opening View of Visual Development
Mo discusses a recent study which observed how early visual experience drives maturation of the visual cortex.

Come One, Come All, and Witness the Molecular MACHINE
Alex admires two papers that describe how proteins are pumped out of cells by the SecA secretory protein.

What Shortage of Scientists and Engineers?
The TierneyLab Blog asks “If the United States really has a critical shortage of scientists and engineers, why didn't this year's graduates get showered with lucrative job offers and signing bonuses?”

Halloween Skeletons and Reactive Chemistry [Sciencebase Science Blog]

Posted: 31 Oct 2008 04:00 AM CDT

A jack-o'-lanternIn the latest scary issue of the chemistry news webzine, Reactive Reports: Dating skeletons, sticky feet for Gecko Guy, volcanic chemistry from the depths of Hades, and chasing mad cows.

CSI: Waco - A statistical method that processes spectroscopic measurements very quickly could allow crime scene investigators to determine time of death of skeletal remains more accurately and quicker than before, according to researchers at Baylor University in Waco, Texas.

Stuck On You - Scientists have long been interested in the ability of gecko lizards to scurry up walls and cling to ceilings by their toes. Now, researchers have found a way to mimic those hairy gecko feet using polymers or carbon nanotubes.

Tubular Reactions - Using surface-modified carbon nanotubes to activate an important industrial chemical, butane, without the need for an expensive metal catalyst—Dang Sheng Su and his team present a process that offers a cheaper alternative to the current industrial process for butane activation.

Chasing Down Mad Cows - Researchers in Europe have tracked down the molecular anchor that hooks errant and infectious prions leading to mad cow disease, scrapie in sheep, and Creutzfeldt-Jakob disease in humans.

Halloween Skeletons and Reactive Chemistry

Five-leaf Clovers [Sciencebase Science Blog]

Posted: 31 Oct 2008 02:30 AM CDT

A four-leaf cloverAn anonymous visitor to the site emailed me: “I found a 5 leaf clover… do you know anything about it? Is it good luck or bad luck?”

It’s just a mutation, like the four-leaf clover, of course. The four-leaf mutation is quite rare occurring once in about 10,000 specimens. Five is rarer still. But, according to this site: Five-leaf Clovers bring extra good luck and attracts money.

Nice, I wonder why the banks don’t breed these things and hand them out to their managers.

Of course, there is no such thing as “luck” and no number of leaves on a member of the more than 300-strong species of plants in the pea family Fabaceae is going to change that. Clover (Trifolium), or trefoil, usually means three-leafed, hence the surprise when one finds a specimen with four, five or more leaflets. The world record clover is an uber clover with 21 leaflets, although the Guinness record site says 18. Wikipedia, in traditional character has both figures on two different pages. Intriguingly, both the 18 and 21 leaflet specimens were found/grown by Shigeo Obara, a farmer in Japan’s Iwate prefecture.

Clover is found across the globe, most species are found in the temperate parts of the Northern Hemisphere, but many also occur in South America and Africa, particularly at high altitudes in the tropics. Clovers are small annual, biennial, and short-lived perennial herbaceous plants. To “be in clover” means to be living a carefree life of ease, comfort, and prosperity. But, if you’re due for a drug test make sure you haven’t been drinking milk from cows fed on clover. Clover has a small amount of morphine, which can end up in bottled milk. Eating clover itself can trigger blood and urine drug tests. It’s one more excuse for unlucky athletes caught abusing the system.

So, what is the origin of the notion that four-leafed clovers are lucky? According to legend, each leaf, or rather leaflet, represents something: hope, faith, love, and the fourth luck. It presumably has some association with the Irish “Shamrock”, which Saint Patrick used as a metaphor for the Holy Trinity of the Catholic fate. the Shamrock having four leaflets forming a single leaf by definition - God the Father, the Son, and the Holy Spirit. Such metaphors are not uncommon in other religions where multifaceted deities are represented this way.

But, the Shamrock
metaphor
doesn’t explain
the luck associated
with the
fourth leaflet
the Shamrock metaphor doesn’t explain the luck associated with the fourth leaflet, if anything one would imagine that a fourth leaflet would represent the Devil and so be bad luck. Although some say it is meant to represent God’s grace. According to the Wisegeek site, when Adam and Eve left the Garden of Eden, Eve is supposed to have carried a four leaf clover. “Curiously, the lore of the white clover plant is also associated with repelling snakes, though it didn’t seem to work in the Garden of Eden,” the site says. I suspect the snake-repellant aspect comes from the Irish St Patrick legend. Ireland famously has no snakes.

One important aspect of the four-leaf clover myth is that for it to bring luck you must find it serendipitously, there’s no point in searching for one and certainly no point in buying one; several websites offer for sale hand-picked four-leaf clovers! However, if you were a child in the Middle Ages who found a four-leaf clover you would have been given the gift of being able to see fairies and plant sprites…

It’s all superstitious nonsense, steeped in the mythology of religion, in dark times there is a deep-rooted (pardon the pun) psychological need to cling to such ideas of a better life beyond the grave and the idea of good luck associated with a symbolic plant simply reinforces such notions and reminds us of the deep-seated need in many people to postpone thoughts of their own mortality. Whoops…got all heavy there. Apologies. It seems that searching for four-leaf and beyond clovers is a perennial favourite among children and if it gets them out in to their gardens or the countryside on a long hike to search for the biggest then that’s no bad thing. Indeed, the exercise and fresh air will no doubt bring them luck by helping to stave off obesity and type 2 diabetes. Just don’t let them pick any dandelions…it’ll make them wet the bed, you know?

The original short version of this post originally appeared on Sciencebase - 2005-05-19

Five-leaf Clovers

Movember [Bayblab]

Posted: 30 Oct 2008 09:14 PM CDT

As the more observant would have noticed already, the month formerly known as 'November' is rapidly approaching.

Starting in Australia, and New Zealand, there's now a fairly large international group of people who call this month 'Movember', and refuse to shave the bit of their face below the nose, and above the mouth for the 30 days. The movement has now spread to Canada, the US, the UK, Spain and Ireland, hopefully there'll be moustaches cropping up all over the globe.


There is a reason for all this... down under November was already 'Men's health awareness month'. Without detracting from the importance of breast cancer, women's reproductive health and wellbeing, and all the other various facets of women's health which were all too painfully ignored until recent decades, it's also worth noting that men suffer from some pretty nasty medical conditions themselves, and often need their own brand of gender-specific care. In addition to breast cancer (which is often forgotten about in men), men also get prostate cancer at an alarming rate (every year 4,300 Canadian men die of prostate cancer), testicular cancer, erectile disfunction and depression.


To quote from the movember website:
"However we look at it, men are far less healthy than women. The average life expectancy for men is five years less than women (presently 77 compared to 82).

Of the 15 leading causes of death among Canadians, men lead women in 14 of the causes. Men are 30% more likely to get cancer, than women, and 55% more likely to die from it. Men's suicide rate is four times higher than that of women. "


Specific to younger men is the problem of testicular cancer (the most common cancer among young men), depression (more women report being depressed yet more men kill themselves), and road accidents (accidents are the second biggest killer of young men).


Men also have this nasty habit of not getting medical conditions looked at, prefering instead to just tough it out. It's just not viewed as 'manly' to go and see the doctor about erectile dysfunction and prostate concerns. This'll only change after a considerable amount of public education... and movember is an important part of this. During movember, people can donate money to encourage a moustache, and this money will all go to various men's health organisations.


I, for one, will be sporting a moustache for the month - there's considerable excitement in the lab I'm in to see what style I'll run with (at the moment I'm leaning toward the 'gripper', but might just sport the classic 70's mo). I'd urge some other people to register on the site, and try to raise some money for men's health.

Halloween special: scary medical instruments [Bayblab]

Posted: 30 Oct 2008 01:53 PM CDT

The British Columbia Medical museum has an online gallery with some pictures of old medical instruments. They have 2600 items from the past 150 years. Let play a game: try to figure out what is the use of the instrument:


1)








2)















3)








4)












5)















  1. Perforator: Holme's perforator with side grip was used for gynecology. Used as last resort for obstructed labor.
  2. Double-Clawed toothkey: dentistry.
  3. Adenotome: otolaryngology. For the excision of the adenoids.
  4. 'Smith's' type haemorrhoid clamp: proctology.
  5. 'Devilbiss' skull cutter with spring: orthopaedics.

Bayblab podcast: Episode21 [Bayblab]

Posted: 30 Oct 2008 12:02 PM CDT

The latest Bayblab podcast is up (mp3 file here, rss feed here). For those of you who have never experienced the bayblab podcast it's one part science, one part dick and fart jokes and one part beer. It's not meant as a replacement for the nature podcast or science podcast but it will cover science news that other podcast do not and it doesn't take itself seriously. It's about making you think and making you laugh just like the IgNobel which we cover in this show along with: selecting for hotness in chilis, why is melamine toxic, political genes, and rubbing one out in the name of science.

2 comments:

Dr.DianaFassett said...

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