Lets get Sequenced!

After browsing the the websites of http://www.23andme.com/ and http://www.navigenics.com/, I am really amazed that there is a competitive, viable market for personal genotyping.  These services (just two of a whole emerging online market) both offer what seems at first glance to be quality genotyping services, but I'll concentrate just on 23andme's product since it is much more affordable (ranging from $99 to $399) compared to navigenics ($999, expensive but seems more robust).

So what is personal genotyping?  Why get it done?  Well, first of all let me explain the difference between genotyping and sequencing.  Genotyping is the process of identifing genetic variants within a genome, in this case using SNPs.  This process is just finding a small fraction of regions in your DNA and comparing them to historical medical data.  Now sequencing on the other hand is laying out all the A, T, G, C's for a large region or whole genome.  For a more in depth but easy to follow tutorial on this I really recommend PBS Nova's flash shows (a little outdated though, but informative none the less).  Sequencing is a lot more robust, expensive, and time consuming, but apparently, according to Ivan from scientificsolutions there is a new company out there that will sequence your whole genome for $5000.

The benefits of genotyping your own DNA is arguable.  In fact, everything I have read seems pretty inconclusive one way or the other.  Regardless, the ablitly to analyze your own DNA against ever-growing medical data of known mutations of certain genes would mean you can see, within reason, if you have a high probability of a developing a specific genetic condition.  Of course, this is not a diagnosis, but may help you predict such diseases as Crohns Disease, Type II Diabetes, and BRCA Cancer Mutations (and over a hundred more, but some are pretty obvious without the testing).

The sites also offer you the ability to compare you data to other people, whether that be family data (but they warn you that you may find out your adopted, lol) or you can just compare against friends to see who is the most genetically superior!

UPDATE:  here is a related article regarding why you may not ever want to get this done. Insurance companies could deny you based on a genetic predisposition to a certain disease!

Firefox upgrade scaring porn collectors

LOL!  I don't know what to say about this article, it speaks for itself.

http://www.pcpro.co.uk/blogs/2009/08/26/porn-collection-put-people-off-upgrading-to-firefox-3/

Check the comments to prevent your porn bookmarks from being discoverred!

Computer Programmers Needed!

Now that biology, specifically genetics, is becoming more automated for the purpose of high-throughput, I have seen more and more job opportunities arise to fill the rift between scientists, engineers/computer programmers.  These liason positions trouble me greatly.  They highlight a major inneficiency within organizations.  You have to hire an excessive amount people to compensate just the terminology gaps that two cross-trained individuals could easily tackle, not to mention that your end products are always full of problems and bugs mainly because programmers do not fully understand what the needs of the biologist are, and biologists rarely understand the limits of the programming languages.

If you're a biology major:  TAKE AS MANY PROGRAMMING CLASSES AS POSSIBLE!!!!  In fact, double major, if you can (or at least minor).  I cannot believe there is not more stress put on this, especially in grad school programs. If you have both degrees, then your marketablility is limitless. 

If you're a CS major and are intersted in working in science:  Take an advanced biology course (and all the prerquisites, of course).  If your programming for a genetics lab, then take a genetics class.  Understand the terminology, and the basic priciples that dictate the science.

UPDATE:  Not an hour after posting this, my boss just asked during a meeting if anyone could write PERL scripts, because our normal PERL programmer just got fired, lol!

Trial for Global Warming???

The LA Times reported yesterday that the largest business lobby, the US Chamber of Commerce, is trying to mimic the Scopes-monkey trial by calling for a hearing regarding the legitamacy of human caused global warming and it's harmful effects on the human population.

Despite an overwhelming concensus among published papers and scientists, the US CoC wants to bring this issue up in court in hopes to create the illusion of "discord" among the scientific community, and ultimately allow their members to avoid paying higher taxes/fines regarding emmision and pollution standards.

The EPA, who is primed to initiate legislation that would make greenhouse gases regulatable under the Clean Air Act, has already called such a hearing a "waste of time", but the CoC may pursue this in a higher, federal court.

CCD marker found for bees

A new marker for Colony Colapse Disorder was found in a study featured in the Proceedings of the National Acadamy of Sciences this week. According to genomeweb; the University of Illinois researchers were using microarrays to analyze gene expression patterns, and found a significant difference in fragmented ribosomal RNA (rRNA) in their guts.

The CCD-affected bees had higher amounts of fragmented rRNA, which could, if infected with a virus, harm ribosome performance; thus hinderring protien manufacturing in the cells.

"If your ribosome is compromised, then you can't respond to pesticides, you can't respond to fungal infections or bacteria or inadequate nutrition because the ribosome is central to the survival of any organism," Berenbaum said in a statement. "You need proteins to survive."

This discovery should be able to lead to earlier diagnosis of CCD infected colonies and brings the whole research-effort one step closer to understanding the underlying factors that cause CCD, a disease that has wiped out massive amounts of bee colonies all over the world.

Synthetic Life

As the UK Times reports, the private scientist Dr. Craig Venter is getting close to creating the first synthetic life. Though the possible applications in the eventual refining of this technique are limitless, are there ethical questions that should be addressed?

I assume that the culmination of his efforts will be misperceived by many people, and that the unknown will once again be feared, ostracized. But there should be a very serious discussion of what is happening.

I really recommend reading the entire article posted by the UK Times.