The DNA Network

Reduce, Refine and Replace [Reportergene]

Posted: 31 Aug 2008 04:08 PM CDT

As a perspective, with in vivo imaging this one will be the last dissected rat.

Image by Natalie Zee Drieu (Craftzine.com)

Posted: 31 Aug 2008 02:19 PM CDT

Slobodan Cekic writes in response to How Much Data is a Human Genome:

Now, please do take a look at your fingertips. You ll see the fine lines of your fingerprint pattern. It is unique, and can be used to identify a human; so fine and even much finer structures are defined in your organism.
Now, how high would be only 3D positional information content needed to describe a human?

You would need to position single cells, define the inner structure of particular cell types, describe the form of single nerve cells (dendrites)…etc

Now how many cells are there in the human organism?

Without any calculation, we can see the information quantity to describe a human in uncounted Terabytes. Human chromosomes contain , as calculated here, 740 MB.

So, why for the God’s sake do we believe that the whole of our hereditary information resides in the genes?

740MB is the size of a reference human haploid nucleotide base string, not the data necessary to describe a mature human.

We believe that most of our hereditary information resides in genes because it does. However, a genome, as you say, cannot possibly fully describe a mature human. A genome is more like a brief mathematical equation used to produce beautifully complex fractal design when fed with ambient noise and interpreted as colors and coordinates on a screen.

Arguably, as other commentators have noted, this isn’t enough to describe a genome. Cytosine can be methylated —like a fifth base. Sometimes, a sequencing machine is unable to assert a base, and an extra bit would necessary to report these “no calls.”

But in reality, humans don’t have a “reference genome.” Almost every cell has its own pair of genomes, and these tend to diverge as they accumulate mutations and errors. To be pedantic, to record your Real and Complete Human Genome, one would have to sequence every strand of DNA in your body instantaneously.

Yet, these trillions of strings of millions of bases can be understood as that 740MB reference human genome like a field full of flowers can be understood as a photo of daisy.

no more press releases please [Reportergene]

Posted: 31 Aug 2008 01:12 PM CDT

Researchblogging.org strives to identify serious academic blog posts about peer-reviewed research with a brand new 2.0 aggregation site still launched. Member from January 2008, Reportergene helps the community in finding posts related to development of new reporter assays. Altough still in its infancy, this way to broadcast scientific news, promises to be an effective alternative to boring press releases.

Federation of Genealogical Societies Meeting [The Genetic Genealogist]

Posted: 31 Aug 2008 12:00 PM CDT

This Friday, September 5th, I’ll be attending the FGS meeting in Philadelphia. I’m excited because this is my first big genealogy meeting (after 20 years of genealogy!), and because I get to sit and watch some great presenters discuss genetic genealogy. The program is here.

I hope to meet some other genealogy bloggers, if any of you are planning to attend!

Is genetic testing useful? [Eye on DNA]

Posted: 31 Aug 2008 07:34 AM CDT

In The Malaysia Star today, Dr. Teo Soo Hwang explores genetic testing as it applies to the BRCA gene for breast and ovarian cancer - Can genetic testing be useful? The paper is printing “a series of four articles by the Cancer Research Initiatives Foundation (CARIF) that explores how genes are linked to diseases, the relationship between genes and cancer, and what is genetic testing and counselling.”

By the way, Malaysia’s government is currently considering a DNA Identification Bill that would require people charged with a crime to submit DNA samples. While this type of law is nothing new in other countries, such as the UK, the introduction of this bill in Malaysia at this time is part of a political brouhaha involving opposition figure Anwar Ibrahim who has been accused of sexual misconduct. His supporters fear that if he were forced to give a DNA sample, it would be tampered with and falsely incriminating results would be submitted to the courts.

Om Prakash says at malaysiakini.com:

The onus must be on those who want to freely give their DNA sample to prove their innocence. Let us not be threatened with another draconian law like the ISA for political and law- enforcement expediency.

We are not ready to just trust anybody yet.

Conclusion: Genetic testing is useful to some and not so useful for others.

Other DNA articles of interest in The Malaysia Star:

Your genes, your health (1st in the series)
Let’s do a CSI

Photo credit: Eye on Malaysia, Lukman Kusuma

How to manage the content of a wiki? [ScienceRoll]

Posted: 31 Aug 2008 07:15 AM CDT

I’ve been a Wikipedia administrator for a long time and I’ve had some edits on medical wikis as well. The reason why I mention it now is that I know exactly how hard it is to manage and supervise the content of a wiki. Before, we used VandalProof, a tool which allowed us to review edits really efficiently. But now we have a supertool, Huggle:

Huggle is an application for dealing with vandalism, written in Visual Basic .NET. It was originally developed by Gurch.

Huggle is a tool for dealing with vandalism. Its nature requires that it is capable of editing pages quickly, and of making many edits in a short space of time. Such features should be used with caution. Use of Huggle by new or inexperienced users is not recommended. Use of Huggle is subject to Wikipedia policies and guidelines.

You can create a whitelist for experienced users and a blacklist for vandals. You can revert the edits and leave warning messages on user’s talk pages with only one click. It’s also possible to review several edits simultaneusly (by opening new tabs).

Here is the manual and you can download it here.

A screenshot from the Wikimedia Commons page

Health 2.0 on slideshow [ScienceRoll]

Posted: 31 Aug 2008 06:24 AM CDT

Jan Martens at Medblog.nl featured an interesting slideshow that focuses on health 2.0. It was presented by Carlton A. Doty through a teleconference.

If Enya Became A Biogeek, This Is What Her Videos Would Look Like. []

Posted: 31 Aug 2008 02:01 AM CDT

Interesting, dreamy YouTube video about All Things Biotech. Sort of a language-free primer on cellular biomechanics from the DNA on up to the petri dish, paired with hypnotic, new-agey trance music. Not going to change the world, but you gotta give it points for trying… Plus, it might give your scientific-literacy-challenged associates something to cognitively grab hold of when they have trouble understanding what a biotechnologist does for a living.

Online Dating [Think Gene]

Posted: 31 Aug 2008 01:23 AM CDT

With the “all-natural new-age herbal remedy” niche has already well-commercialized, what territory shall the ambitious huckster stake? Fortunately, the brash misapplication of science spews an unending stream of hopefully salable magic.

Now, two new online dating services promise to find your “scientific match” by testing your DNA.

[note: manually enter links; I will not promote dubious sites with html links which are rewarded by search engines and referral traffic]

The least dishonest (and most expensive) is Scientific Match [scientificmatch.com]. For a mere $1,995.95 and cells scraped out of your cheek, you too can be “physically chemically” matched to your magic sweetheart… that is, if you’re not a felon. Scientific Match is quite adamant about this in their terms and conditions. By comparison, a 23andMe genomic test is $1000, a test which is by all indications is a vastly more comprehensive and scientifically-reputable test. (Scientific Match does not explicitly state for which genes they test and how they interpret results.)

So what exactly does Scientific Match test? From http://www.scientificmatch.com/html/about_physical_chemistry_defined.php :

Physical chemistry is based on the immune system. When we analyze your DNA, we look exclusively at your immune system genes. So, quite literally, when we say that two people have "chemistry", we're saying that their immune system genes are perfectly matched with each other.

By perfectly matched, we mean different. After we analyze your DNA, we match you with other people who have different immune system genes from yourself.

So, encouraged by one weak study about girls smelling sweaty tshirts, they test a few random genes associated with the major histocompatibility complex, match people different test results, and then throw all that crap out and match people willing to pay $2000 for a dating service “based on science.”

Just to be clear, we don’t know of any scientific evidence suggesting that our technology will predict who you’ll fall in love with or even be emotionally attracted to. But the experts clearly see incredible potential in the power of chemical attraction.

…

As long as you're matched with the right person, and you've got chemistry, then it doesn’t matter if it’s via your sense of smell or some (possibly other) chemical sensing system. The fact is, chemistry–and its effects–is real. The specific communication process, though, has yet to be definitively proven

Oh right! Just redefine “chemistry” to mean “anything” and “then it doesn’t matter!” Yet, what has been proven is that if you’re willing to spend $2000 on a dating service, you’re probably willing (and desperate enough) to believe that it works. Therefore, it probably will.

The Scientific Match’s competitor is the shabbier and cheaper Gene Partner [genepartner.com]. Gene Partner is like Scientific Match except that it costs a mere $200, its website sucks, and it’s “in collaboration” with the “Swiss Institute for Behavioral Genetics”. Hilariously, from the “Swiss Institute’s” website [sibeg.org]:

SIBeG is affiliated to GenePartner GmbH (Switzerland) which reserves the right to patent any profitable findings prior to publication.

Surprisingly, SIBeG has yet to publish any research. Hm…

The science may be bunk, but do these services work? Popular online dating review forums make no mention of these services. My suspicion is that because the expenses of running a website and outsourcing simple genetic tests to labs are negligible, and thanks to the generous media blitz by the gullible prole American media, both sites will continue to scratch out a small profit on the internet until their founders get bored. Thus, gullible singles will continued to be matched with about the same rate of success as sites with comparable service fees and web interfaces for the next ten years or less. Hooray for the miracles of genomic science.

Note: the New York Times also mentions the “sweaty tshirt and dating” study. Ok, I admit, it’s a facinating subject, but sorry, the science doesn’t exist yet.

Join the Movement and Stand Up To Cancer [Highlight HEALTH]

Posted: 30 Aug 2008 10:24 PM CDT

Stand Up To Cancer (http://www.StandUp2Cancer.org) is an initiative to raise philanthropic dollars for accelerating ground breaking research through an unprecedented collaboration uniting the major television networks, entertainment industry executives, celebrities and prominent leaders in cancer research and patent advocacy [1]. On Friday, September 5th, at 8:00 pm EST and PST, ABC, CBS and NBC will donate one hour of simultaneous commercial-free prime time for a national fundraising event.

In 2008, over half a million Americans are expected to die of cancer, more than 1,500 people a day [2]. Cancer is the second most common cause of death in the U.S., accounting for 1 in every 4 deaths. Nevertheless, since 2003 the U.S. government’s cancer research budget has been cut every single year. This lack of funding stifles innovation and delays or halts treatments from getting to patients. This has become a critical issue: I’ve written previously about Flat Funding of Biomedical Research and The Threat to America's Health and the Funding of Childhood Cancer, NF Research in Jeopardy.

The purpose of Stand Up To Cancer (SU2C) is to reverse the downward trend in funding of cancer research, to make cancer part of the national debate and to enable cutting-edge research aimed at finding a cure to all types of cancer, including breast cancer, prostate cancer, colorectal cancer, lung cancer, liver cancer, neurofibromatosis and more.

The group leading SU2C includes CBS Evening News anchor and managing editor Katie Couric, Sherry Lansing, Laura Ziskin, Ellen Ziffren, the Entertainment Industry Foundation (EIF), the Noreen Fraser Foundation and the American Association for Cancer Research (AACR).

The landmark television event, Stand Up To Cancer, is designed to rally the public and raise millions of dollars for cancer research. 100% of the money raised goes towards accelerating the course of cancer research. Funds will be streamlined through an innovative funding and distribution model directly to scientists. The following video, “Where the Money Goes”, provides an explanation of SU2C’s research funding model.

You can read more at the Stand Up To Cancer web site. For microbloggers, you can also follow SU2C on Twitter.

This historic television event to enable cancer research cures will simultaneously air, commercial free, on all three major networks Friday, September 5th at 8:00 pm EST and PST. I’m actively involved in cancer research and can attest to the difficulty in getting funding. I encourage you to tune in and support the next generation of groundbreaking cancer research.

References

ABC, CBS, NBC announce historic collaboration to “stand up to cancer”. Stand Up To Cancer press release. 2008 May 28.
Cancer Facts & Figures 2008. American Cancer Society. Atlanta, Ga. 2008.

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