Do genes blog?

New research suggests that groups of genes talk to each other and pass the message down to next generations of cells. This is being described as “conditional memory” by Georg Fritz at University of Cologne and reported in MIT’s Technology Review’s Physics ArXiv blog.

http://www.technologyreview.com/blog/arxiv/25775/

Reflections on DNA Complexity

DNA over simplified or more complex?

In 2001 deciphering the human genome was thought to be a simple description of the parts list of a cell. Back then we thought simple translation of DNA would explain most of life and that each protein was the result of DNA being copied into RNA and then into amino acids and packaged as proteins. At that time I drew a picture attempting to describe that there would probably be much more complexity and variety. In my job as a nutritionist who sees many oncology patients it was clear to me that cancer cells were different by definition. I wondered why there wouldn’t be many other cells in our body in the process of deciding if a mutation or change in the DNA would remain or be edited out? Why wouldn’t our daily interactions with the outside (and inner) worlds affect this? Also, as we age wouldn’t these interactions impact and modify the text of our DNA like a copy editor(s)?

Learning the DNA complexity

Today we are learning that complexity is much more likely than simplicity in any of our explanations about DNA. First of all, did you know we have two types of DNA not just one? Ancient integration of bacteria is thought to be the reason why we have mitochondrial DNA not just nuclear DNA. These are single strands located in the power houses of each cell and found in huge quantities in liver and other highly metabolically active cells. With such a high level of turnover it makes sense that there would be a lot of modifications simply because of inaccurate or inefficient copying and repairing. Another factor is the addition of regulating “tags” such as methyl groups, called epigenomics. This is not well understood but apparently very important. Another reason that simple explanations no longer work is that it appears that rather than being randomly assorted, DNA strands in each chromosome show a wide variety of selection with some being determined by evolutionary pressure and whether of paternal or maternal origin. This is called imprinting.

Level of complexity

Some people find this level of complexity simply too much to ponder – rather like thinking about the vastness of our universe (part of a larger multiverse). Linear, logical thinking no longer describes the sophisticated biological systems that so elegantly explain life. A leading to B leading to C just doesn’t do it any more. But, we don’t need to understand astrophysics to appreciate a sunrise or sunset. I am in awe of how each time a discovery is made about genomics there is further complexity to impress us. The challenge from my perspective is how to drill down to what is meaningful and valuable for improving our health without being overwhelmed and switched off to the whole process just because it is so detailed.

Another layer of DNA

Another layer to add to this challenge is how each of us approaches discoveries from different personal histories and personalities. What I find fascinating may just be plain boring to someone else.

  • I would love to hear from you – what do you think about it all?
  • Are you uncomfortable or stimulated by this level of complexity?
  • Do you see chaos or order or perhaps both at the same time in some kind of dynamic equilibrium?

Body fat as a safe storage site for toxins?

The late Roslyn Alfin Slater, PhD, one of my mentors at UCLA, noted that adipose tissue is a relatively safe place to store toxins that aren’t readily removed (by liver or kidney detoxification processing). A recent examination of NHANES (National Health and Nutrition Examination Survey) showed a highly significant correlation between six environmental pollutants in serum and weight change. A second study found similar changes in 39 obese individuals subjected to a 15 week low calorie diet and looking at 26 organochlorine compounds in blood and body fat (subcutaneous). This underscores the importance of supporting liver and kidney detoxification processes by eating a high fiber, fruit and vegetable rich diet and avoiding environmental pollutants for health.

Int J Obes (Lond). 2010 Sep 7

Int J Obes Relat Metab Disord. 2000 Oct;24(10):1272-8.

Sit less – move more but it may be all in the genes!

First we learn that it is less about what you do rather how little you sit down that affects your health and mortality. Sit less, move more! (Patel, et al. Am J Epidemiol 2010:172(4)419-429)
Another study (with mice not humans) indicates that voluntary exercise is highly heritable meaning wanting to sit more may be something you are programmed to do (Garland, et al. Proc Roy Soc 2010, DOI 10. 1098/rspb2010,1584). Even if that is the case for humans (and many rodent behavior studies don’t pan out when applied to humans) then it simply means for those of us who find it hard to get to the gym we will still benefit if we get up, pace around and are just more active. “Use it or lose it” as Jack Lalanne would say – one of my heroes who is still amazingly active both physically and mentally in his 90’s. Go Jack!

Experimenting in the Kitchen

Listening to Jeff Potter, a software engineer and author of “Cooking for Geeks” as he demystifies food preparation as Ira Flatow’s guest on Science Friday. Who knew that “Total Textural Preference” describes how one of the proteins in meat (Myosin) changes shape before the other one (Actin) at 120 degrees and apparently we like that?!
Did you know that when it is hot enough to fry an egg it means the sidewalk is at least 142 degrees? I also learned that sugar melts at 367 degrees. I forgot that food science was so interesting. My undergraduate courses never held my attention like that but perhaps it is all in the delivery and Jeff is a self professed kitchen geek. I can’t wait to read his book and start experimenting in the kitchen.

Mushrooms as health communicators

Mushrooms are a large and ancient group of fungi in their fruiting stage. Reseearch is now suggesting that fungi in both their vegetative and fruiting stages play a role in intestinal immunity. Alpha glucans are found in larger concentrations in the vegetative stages whereas it is the beta glucans in the fruiting mushrooms. White button mushrooms may be particularly helpful in antiviral activity according to a new study funded by the USDA http://www.ars.usda.gov/is/pr/2010/100729.htm

23andMe receives more funding

Google has invested 7 Million total (2.6 Million more today) in 23andMe believing in its capacity to deliver in the future. With the number of participants and data collected this may well be true however on the day 23andMe announced they had partnered with another company to provide genetic counseling I am confident that my expertise will be recognized for its value. We all eat but once you learn your perceived risk for a disease that’s all to learn. I integrate this data to provide action plans, tailored recipes and make this knowledge helpful and proactive.

Validation of Genomic Data becomes Crucial

One reason why the genomic revolution is not yet as advanced as many had hoped is the huge amount of variability between individual genomes and challenges surrounding data validation.

At a recent meeting of Human Genome Organization (HGM) in Montpelier, France a number of presentations noted the widespread variation among human genomes that are challenging the current high throughput technologies.

Validation protocols for the 100 sample genomes required to win the Archon Genomics X Prize will require highly sophisticated bioinformatics software to capture this inter-individual variability. Simply conceiving of such variability mentally is already enough to give one a headache!

Unrealistic expectations lead to disappointment for genomics

Nicholas Wade, science writer for New York Times describes his disappointment in genomics for personalized medicine but this misses the point in my opinion. Genomic discoveries like any diagnostic tool are part of a larger picture of health. It is in integrating this knowledge along with family medical history and personal life experience that true medical advances will be realized. Over reliance on any screening tool is bound to lead to disappointment especially when people come at the field with such high expectations. Identifying individuals using DNA is a very different project than identifying their risk factors for chronic disease beyond what we already know to be true – smoking, being overweight and sedentary, etc. Mitochondrial DNA and how it influences gene expression is another dimension of genomics yet to be understood or integrated into nuclear DNA genomic discovery. If mitochondria are relics of symbiotic bacteria then this would probably be highly relevant to our current health status. I think we have to be patient and continue to use sensible public health applications while slowly integrating what is valuable from genomic scientific discoveries. Just my personal view – I’d be interested in what others think.

http://www.nytimes.com/2010/06/13/health/research/13genome.html?src=me&ref=health

Single Molecule Sequencing (SMS)

Helicos Biosciences Corp. is advancing single molecule sequencing http://www.helicosbio.com/Technology/TrueSingleMoleculeSequencing/tabid/64/Default.aspx

Stanford professor Stephen Quake has made his entire genome available for research purposes using SMS. One more step towards cheap and available GWAS for all. Lee Hood and George Church are members of Scientific Advisory Board.