Can Patients Understand their Own Genome?

I just ran my 23andme SNP data (Single Nucleotide Polymorphism: basically, the distinct mutations that make my DNA unique) through geneticgenie.com, a website that puts the number and type of mutation in a handy table.  The website also provides nutritional recommendations based on the presumbed metabolic impact of my particular mutations.

However, after feverishly researching biochemistry I have some concerns with Dr. Yasko's conclusions cited on that site and others. These websites appear to make a number of biochemistry mistakes, and I'm not seeing a lot of citations to original research, just a lot of unpublished "physician observations".



A selection of results from G enetic Genie. There are two copies of most genes in our genomes (one from our father, one from our mother) and one or both may be mutated. The color-coded results show that I have two mutated copies of several important genes (colored red) involved in neurotransmitter metabolism and other core biochemical processes. I also have two genes with one bad copy (yellow),


Some of the statements about, for example, BH4, appear to be incorrect. Genetic Genie states that impaired BH4 production or increased BH4 utilization can impact ammonia detoxification in the urea cycle, but BH4 is not directly involved as a cofactor in ammonia to urea conversion. Instead, BH4 is involved in one of at least two pathways for generating citrulline. (Citrulline is regenerated in the urea cycle to turn ammonia into urea.)


Not to say they're not doing good work, but you have to interpret biochemistry in context. For example, I am homozygous for a mutation in CBS, which they say would upregulate CBS activity and lead to increased cystathione, cysteine, and eventually to increased taurine and sulfite. But I also have a heterozygous mutation in CTH, which would limit the amount of cystathione converted into cysteine, effectively stopping that cascade at the starting line.

I hope we're just a short ways off from a website or interface that can actually map all of our unique (SNP-dependent) metabolic pathways, but I think we're still in the dark ages when it comes to interpretting SNP genome results. Promethease is the online tool that has replaced 23andme's health-specific genetic information, but the website only summarizes Pubmed results:



The Promethease website is great, but is based on observational studies with tiny effect sizes. Trying to infer causation from those correlational studies is a textbook example of how not to interpret statistics.

Faced with the complexity of ~20,000 SNPs and less-than-user-friendly professional tools like ENSEMBL, I don't think it is possible for individuals to understand how SNPs influence protein function to the extent necessary to make informed decisions about our biochemsitry.

Core biochemical methylation pathways.

Two common mutations can cause decreased levels of BH4. The first mutation increases the activity of CBS, which converts Homocysteine to Cystathione and eventually to cysteine and then taurine.  The second mutation is directly involved in the regeneration of BH4 in the methylation pathway.

But before I get ahead of myself, why is BH4 so important?

Tetrahydrobiopterin (BH4) has five major responsibilities as a cofactor.  It is needed to work with:

Tryptophan hydroxylase (TPH) for the conversion of L-tryptophan (TRP) to 5-hydroxytryptophan (5-HTP)
Phenylalanine hydroxylase (PAH) for conversion of L-phenylalanine (PHE) to L-tyrosine (TYR)
Tyrosine hydroxylase (TH) for the conversion of L-tyrosine to L-DOPA (DOPA)
Nitric oxide synthase (NOS) for conversion of a guanidino nitrogen of L-arginine (L-Arg) to nitric oxide (NO) in the Urea Cycle
and
Alkylglycerol monooxygenase (AGMO) for the conversion of 1-alkyl-sn-glycerol to 1-hydroxyalkyl-sn-glycerol

The first three reactions are critical to producing adequate levels of serotonin and dopamine. Low levels of BH4 can impair neurotransmitter production and lead to the build up of toxic intermediates, like phenylalanine.



This chart shows that without BH4 phenylalanine (found in all foods) is not converted to tyrosine. Tyrosine one of the 22 amino acids used to build protein and is normally non-essential. It is found in most foods.

BH4 is synthesized in four ways:



BH4 is involved in the major biochemical cycles:



Methionine is a major source of sulfur groups in the diet, so limiting methionine-rich foods helps limit problems from an overactive transulfuration pathway (i.e. overactive CBS enzyme). Other sulfur rich foods include crucifer vegetables and onions and garlic.

BH4 is tangentially involved in both the urea cycle and the folate cycle.

The urea cycle in detail: Arginine from our diet or from protein metabolism is converted to ornithine and urea by the enzyme Arginase. Ornithine is then converted to citrulline by ornithine transcabamoylase (OTC). Citrulline is converted back to arginine. This cycling of Arginine through the various intermediates is what converts ammonia to urea. (More info)


Source.

Arginine is also required for the production of Nitric Oxide (NO) by the enzyme nitric oxide synthase (NOS or eNOS). This reaction is dependent on the levels of BH4 available from the BH4 cycle. Remember two molecules of BH4 are needed to generate Citrulline and NO. One molecule of BH4 will in turn generate peroxynitrite and if there is no BH4, super oxide is formed. (Source. )

The Urea Cycle and the Nitric Oxide Cycle are interconnected by arginine as follows: Citrulline, made from ammonia (and ornithine), is recycled to arginine in the Urea Cycle. That arginine can then enter the Nitric Oxide Cycle where it is converted to nitric oxide by nitric oxide synthase using tetrahydrobiopterin (BH4). (Note that citrulline is also generated during the formation of nitric oxide from arginine.)

From this we can conclude that a deficiency in BH4 does not impact ammonia detoxification in the urea cycle.

How Many Great- (Great...) Grandparents Did I Have?

Ancestry studies based on mitochondrial or Y chromosome assays only detect a single path through our complicated family tree.  For example, my Y chromosome is inherited from my father, and my father's father, who got it from his father's father's (...) father.  A test based on my Y chromosome wouldn't take into account any of the rest of my ancestry contributed from, for example, my father's mother's father's (...) father).

So maternal and paternal lineage data is really about just two branches picked out of our entire family tree.  The results are presented using "haplogroups", which are unique patterns of mtDNA or Y DNA that can be traced back to a single mutation event.  But ancestry is exponential, not linear! Haplogroups only detect a single branch out of a very large number of branches.  And what if my family tree isn't a tree, but a bush?  The scientific term for this is "pedigree collapse".

Assuming a generation time of 20 years, 500 years ago (=25 generations) I could have had 33 million great [...] grandparents! But the population of Europe (I have European ancestry) was only around 60 million in A.D. 1500 (Jan de Vries, compilation of estimates). Assuming no interbreeding of ancestors in the last 500 years, I would have to be related to everyone with European ancestry a little over 25 generations ago. Clearly there must have been some interbreeding, which would imply that I did NOT have 33 million great [...] grandparents.

This probably explains the question better than I can.  

I think the key question is...How many great [...] grandparents did I have? THAT would tell us how informative mtDNA or Y-chromosome haplogroups are.  If I had more grandparents then these tests are less informative.  If I had fewer grandparents they could be quite informative.

I'd be curious just to know ballpark figures. Did I have 10 million or 10,000 great [...] grandparents in A.D. 1500?

I found a study that shed some light on this issue: The Geography of Recent Ancestry across Europe by Peter Ralph and Graham Coop.  According to their results, there was a genetic bottleneck in, for example, the Balkans, around A.D. 1400 and a much larger bottleneck around B.C.  100.  This means that, for example, two average unrelated people in Europe share almost all of the same ancestors as recently as 1,000 years ago!

Top Conservation Stories of 2014

Here are a few of the most important conservation stories from 2014:

--Gila River Proposed Diversion approved by ISC

--Mexican Gray Wolf critical habitat expanded to include most of NM and AZ south of I-40

Zone 1 is where Mexican wolves may be initially released or translocated.  Zone 2 is where Mexican wolves will be allowed to naturally disperse into and occupy, and where Mexican wolves may be translocated.  Zone 3 is where neither initial releases nor translocations will occur, but Mexican wolves will be allowed to disperse into and occupy....where Mexican wolves will be more actively managed...to reduce conflict with the potentially affected public.  However, in AZ east of Highway 87 there will be a "phased approach" to managing wolf populations.

--U.S. Congress Omnibus spending bill approves the Resolution mine landswap in AZ, grazing lease terms expanded to 20 years, and Valles Caldera becomes newest National Park

--Drought in CA (7% snowpack) ... and NM.  (e.g. Heron Lake resevoir levels fall, fail to make San Juan-Chame deliveries to Rio Grande)

-- US EPA and NRCS try to regulate agriculture under CWA....and fail.  The problem of increasing toxic algae problem in Ohio lakes came to a head in 2014 when Cleveland had to turn off their city water intake from Lake Eerie due to a toxic algal bloom. The proposed rule would have allowed EPA to regulate "non-point source" water pollution from farms that did not have a NRCS-approved conservation practices in place.  But apparently the outcry was too much, and early in 2015 the rule was amended.  Note that the final rule, even though it no longer contained this provision, was still vehemently protested in 2015.

--  Gunnison Sage Grouse listed as "Threatened" under the ESA, Colorado appeals.

-- Colorado River Pulse....mostly just grows more tamarisk.

--  Pleistocene megafauna extinction due to meteor impact, new study finds.  

-- Wilderness turns 50 years old

-- New "stacked trait" GMO potatoes and soybeans approved in the U.S.

And a random tidbit:  rabbits eat more forage in utah than bison...leading ranchers to question the state's continued bounty for coyote skins.

Don't Read This if you Trust Me: The Pitfalls of Trusted Sources

Keith Kloor reports that Daniel Kahan recently "said that 'people misinform themselves.' What did he mean by this? Well, people have go-to sources for issues they don’t have time (or the inclination) to research. Your go-to source on a contentious issue–such as climate change or GMOs–is likely to share your values. That affinity is what makes the source trustworthy to you. But that doesn’t mean your trusted source is necessarily going to provide you with correct information."

I disagree for two reasons: 1) That's not quite what Kahan is concerned about, and 2) I think there are some information sources that are able to resist ideological decisions -- and we would do well to turn to them in times of misinformation.

1)  Kahan has an excellent blog where he tries to explain his often counter-intuitive research.  For example: a study he conducted evaluating the relationship between numeracy and ideology.  He looked at a person's ability to detect statistical covariance in case studies that were value-neutral versus case-studies about hot-button topics like abortion and gun control.

Not surprisingly, people had a harder time correctly interpreting data about hot-button topics.  To be specific, people failed to properly analyze data when it conflicted with their ideology.  

Kahan likes to say that "critical reasoning is being used opportunistically."  And he goes on to point out that more proficient people (i.e. more proficient at value-neutral numeracy tasks) are more polarized than less proficient people, not because they are more biased (although this may be true) but because they are better at fitting the evidence to their existing ideological biases.  Importantly, this effect appears to be equivalent on both sides of controversial topics.  Neither liberals nor democrats have a monopoly on crazy baseless beliefs.

2)  This brings me to my second point.  Perhaps there are a group of people who are not liberal or conservative; people who do not have strongly-held opinions about anything apart from what the evidence provides.  Probably more people would self-describe themselves in this group than can actually live up to this standard, but still.  It seems to me that this would be the ideal of a dispassionate, objective observer.  A true scientist.  And if our go-to sources are value-less, or better stated, if our go-to sources hold objective knowledge as their highest value, than we are justified in turning to them for information.  Doesn't mean they can't be wrong, but if they have the characteristics I mentioned previously, then at least they are thoughtful, transparent, and open to conflicting data.

Presumbably Keith would support this second point, if he wants us to keep reading his blog!  However,  Keith Kloor goes on to point out that even trustworthy sources can hold fallacious viewpoints: "Groups like Greenpeace and thought leaders such as Michael Pollan, Vandana Shiva, and Bill Nye have enormous clout in their respective spheres. "  These people and groups earned this clout by speaking truth to power.  But that doesn't mean all of their opinions are objectively justified.  People can be rational about some topics, but irrational about other topics! 

How To Find The Truth (on the Internet)

I recently read about two different meta-review techniques: the Total Evidence Approach and the Quality Analysis Method, and that got me thinking about information processing and knowledge creation in our information-saturation internet-era.  How do we find the truth on the internet?

"In the total evidence approach (Kluge 2004; Sherman et al. 2008) all information is considered and data are not weighed by quality of evidence. Although the total evidence approach is subject to the biases and errors of individual studies, we deemed it preferable to the alternative “quality analysis” method (Sherman et al. 2008) in part because of the difficulty of objectively evaluating the relative validity and quality of the widely heterogeneous data sets that we reviewed."  Source.

I think we can all agree that a total evidence approach isn't going to work very well on the internet: there is simply way to much junk to try to average out truth from the hubbub.  But how to engage a quality analysis?  Michelle Nijhuis describes an iterative process of fact-checking in journalism, wherein she continually seeks out new sources to comment on and counterbalance other sources, until ideally, after an infinite(!) number of steps, truth is reached asymptotically.  But she admits this approach is time-intensive and unwieldy.  Furthermore, this approach can lead to the problem of "false objectivity":  journalists actively obscure truth when they try to objectively treat controversial issues by giving crackpots equal weight with experts and scientists. 

Instead,  I use a balance of evidence approach to truth-finding in science debates: I read widely and then select trustworthy sources.  If a person or organization publishes unsupported or erroneous information, I tend not to give them a second chance.  Also, sources that don't include open debates are outed as substandard information sources and discarded from the analysis.  A process of winnowing results, and after several months (years) of research, only the best sources are left standing.

Typically, the best sources are: experts who publish in-depth analyses of primary sources (e.g. journal articles).  They are open to quality comments from a range of voices, and their work is therefore continually self-correcting. 

Interestingly, I often prefer blogs over than traditional journals in my research.  Bloggers can attain higher standards of truth than the peer-review system.  Journals are slow to correct mistakes and often don't include enough discussion to reveal divergent viewpoints.  

What Causes Colon Cancer? More importantly, what prevents it?

Colon cancer incidence --like that of many cancers-- varies several-fold between different countries, indicating that perhaps there are environmental or lifestyle factors that cause or prevent it. Much of this post is based on this excellent review article

Known Influences of Colon Cancer Risk (ranked from most important to most equivocal)

Aspirin: The Women's Health Study of 34,000 women 45 years and older found a 42% reduction in colonrectal cancer in the group that was taking aspirin.

Selenium: Populations with adequate selenium intake (most of the U.S. is OK, but European soils are selenium-depleted so their foods are lower) have lower colorectal cancer.

CLA, or conjugated linoleic acid is protective against cancer and found in grass-fed beef and dairy products, possibly explaining a lower incidence of colorectal cancer among people who eat dairy.

Dietary fat: results are conflicting. While a study based on a large, hospital-based sample of cases and controls, provided no evidence that dietary fat was associated with increased risk15, an equally large and well executed case-control analysis revealed a strong association of dietary fat with colon cancer risk 16.

Fiber: results are conflicting. One of the best studies of diet and colon cancer, the prospective Nurses Health Study, indicated that dietary fiber does not affect the risk of subsequent colon cancer 17. Although some fruits and vegetables, which contribute fiber to the diet, may be protective, dietary fiber alone appears to have no impact on colon cancer risk17.

Vegetarian Diet: while eating a vegetarian diet slightly lowers the risk of all cancers, it has also been found to increase the risk of colon cancer, according to the European Prospective Investigation into Cancer and Nutrition (EPIC) study.

Meat: results are conflicting, and different for different types of meat.  “The available epidemiologic data are not sufficient to support an independent and unequivocal positive association between red meat intake and CRC [colorectal cancer].” - from a review of the evidence regarding red meat consumption and colon cancer in the European Journal of Cancer Prevention [1]. Cited by Dr. Briffa.

However, a number of compounds in meat are known to be harmful.  For example, heterocyclic amines, a known cancer-promoting substance, are produced when meat is grilled or fried at high temperature.  High iron levels may induce oxidative stress and can be harmful.  Meat increases IGF-1, which promotes growth of all cells, esp. cancer. Recently, a sugar in red meat called Neu5Gc has been linked to inflammatory effects.  And even Carnitine, a heart-healthy compound found in red meat, has been found to stimulate bacteria to produce TMAO, a known cancer-causing substance.  However, whether all of these individual compounds, when consumed as part of a healthy diet, cause cancer, has yet to be determined.   Chris Kresser has comprehensive review article that addresses these complexities in greater detail.  

[1] Alexander DD, et al. Meta-analysis of prospective studies of red meat consumption and colorectal cancer. Eur J Cancer Prev. 2011 May 2

Is Organic Agriculture Healthier for the Environment and the Consumer?

This deceptively simple question is difficult to prove.  In a widely-read science blog post, Dr. Christie Wilcox (her PhD is in marine biology, not agriculture) argues that the supposed benefits of organic farming are all myths.

While some of her specific claims, such as that organic farmers are allowed to use the incredibly toxic natural compound rotenone, are off-mark, much of her critique appears to stand.  The reasons are various, but telling:  there are costs and benefits to different agricultural systems, and organic farms face many of the same challenges of conventional farming.  For example, herbicides allow no-till farming, with myriad benefits for soil structure and water quality.  It is extremely difficult to practice no-till without some means of removing weeds.

Certified organic farms may not use synthetic pesticides, herbicides, fungicides, etc.  But if organic farmers choose to use a natural compound to kill weeds or pests there is nothing to guarantee that such a compound would be less toxic to the ecosystem and to humans. Natural compounds on organic farms may be more toxic than their synthetic analogues!

Unfortunately, while there are comprehensive databases of the type and amount of pesticides found on conventional food (see the Environmental Working Group's annual Dirty Dozen list), no such testing of natural compounds on organic produce is conducted.  Apparently synthetic compounds are investigated more than natural compounds, perhaps due to an unstated belief in the Naturalistic Fallacy, i.e. that natural chemicals must be healthier than synthetic chemicals.  But many plants (for example, nightshades) contain totally natural compounds... that are totally toxic as well.

A good take-home message would be to wash all of your fruit and veggies, whether they are organic or not.  And learn which plants are poisonous.  I'm not even going to get into all of the (natural and synthetic) chemicals and preservatives in grains, let alone refined flours, etc.

Pathogenic Bacteria Mediate Inflammatory Effects of Meat

A recent study from Harvard university concluded that, in genetically susceptible mice, dietary saturated fatty acids (SFAs) led to increased pathogens in the gut. (See Rob Wolf's critique of the study.)  The implication appears to be that dietary SFAs feed harmful microbes.  A similar conclusion was also reported for choline...

Researchers have theorized that the evolutionary pressure from pathogenic gut bacteria has led to the link between SFAs and a prophylactic inflammation: our bodies ramp up a defense response to SFAs because these fats feed harmful bacteria.  In contrast, monounsaturated fats (MUFAs) and polyunsaturated fats (PUFAs) are actually antimicrobial.  

However, it appears that pathogenic species are not being stimulated directly by dietary fats, but rather by cholesterol in our own bile.  This makes sense, because most fats should be absorbed before they reach the large colon, but bile is one of the largest inputs to our large intestines.  If this is true, than dietary fats are not the culprit so much as our own bodies' reaction to SFAs.

Even so, the association between saturated fat intake and inflammation has been repeated numerous times.  For example, one study of obese women on a high-fat low-carb diet noted 25% increase in C-reactive protein (CRP, a marker of inflammation) compared to a 43 decrease on a low-fat high-carb diet.  But when I searched for studies confirming this, I found a 2008 study from the University of Aukland, New Zealand, found that in healthy men, a single high-fat (71% of calories) meal did not lead to changes in tumor necrosis factor-α (TNF-α), and CRP.  Also, a 2004 study looking at the acute effect of a high-fat (50% of calories) meal in young healthy men noted no significant changes in CRP.

Jeff Leach at the Human Food Project lays out an interesting theory to explain these divergent results:

"Multiple studies have shown that a high fat diet produces low-grade inflammation, which in turn promotes metabolic disease such as diabetes. Interestingly, the low-grade inflammation correlates with circulating levels of a plasma endotoxin known as lipopolysaccharide (LPS). LPS is the primary structural component of the outer membrane of Gram-negative bacteria. Importantly, LPS only originate in the gut."

He concludes that intestinal permeability and the translocation of inflammatory toxins occurs only in the absence of Bifidobacteria, a type of beneficial bacteria found in mother's milk and fermented dairy products.  Importantly, stimulation of these species with fiber prebiotics like FOS and inulin has been shown to block inflammation from saturated fats.  Indeed, higher dietary intake of fiber has been repeatedly associated with lower markers of inflammation.

Take home message: always eat enough fiber with higher-fat meals.

A Disturbing History of Nutrition Science

What is the biggest mistake scientists have ever made?  Nina Teicholz's The Big Fat Surprise, a wonderful history of the awful state of nutrition science, suggests that science's worst mistake may well be the idea that saturated fat is unhealthy.  She makes a convincing case that nutritional guidelines over the last half century, by focusing on fats rather than sugars, have resulted in the premature deaths of millions of Americans and others around the world.

Even more interesting than turning conventional wisdom on its head, this book is an eye-opening journey into how an entire field of science can be hijacked by special interests and strong personalities. Moreover, this book holds important lessons about how the process of science is still susceptible to the same biases and group-think as the rest of society.

Nina Teicholz sums up the story of how nutrition science went wrong:

"Well-intentioned experts, hastening to address growing epidemics of chronic disease, simply overinterpreted the data. Scientists hypothesized that dietary fat was to blame...  This hypothesis became accepted as truth before it was properly tested.  Public health bureaucracies adopted and enshrined this unproven dogma.  The hypothesis became immortalized in the mammoth institutions of public health.  And the normally self-corrected mechanism of science, which involves constantly challenging one's own beliefs, was disabled.  While good science should be ruled by skepticism and self-doubt, the field of nutrition has instead been shaped by passions verging on zealotry. ...Once ideas about fat and cholesterol became adopted by official institutions, even prominent experts in the field found it nearly impossible to challenge them."  

"What I found, incredibly, was not only that it was a mistake to restrict fat but also that our fear of the saturated fats...has never been based in solid science.  A bias against these foods developed early on and became entrenched, but the evidence mustered in its support never amounted to a convincing case and has since crumbled away."

Let the sorry story of nutrition science be a lesson for the scientists and promoters of scientists in other fields.  We like to think that science is independently and objectively building a tower of knowledge for the ages, one rock at a time, but the reality is that our science is a product of our society, our beliefs, our biases, and our assumptions.

Ketosis!

Many people, even biologists, don't know about ketosis, the alternate method our bodies have for supplying energy.  Most people (especially in modern society!) utilize glucose as their cells' primary energy source.  But, in the absence of carbohydrates, our bodies are able to burn fat.  The fats that circulate throughout our body during fasting or very low-carb dieting are known as ketones:

Source.

The metabolic changes necessary to metabolize ketones instead of glucose depend on human physiology and activity:

These graphs describe Peter Attia's experiments with different exercises while in ketosis, and the results to his blood glucose, ketones (B-OHB) and lactate levels. 

Blood Glucose Charts

From wikipedia article on diabetes.

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Interesting behavioral health article on hypoglycemia and anger, violence.  

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Fast versus slow oxidizers (=induced hypoglycemia).  This website basically recommends eating more fat and protein if you have these below-normal glucose excursions.