The above images are eigenfaces … which are statistically distilled basic components of human faces … from which ANY human face can be reconstructed as a combination of the above basic components.  It’s a great mathematical trick – particularly if you’re into the whole mass surveillance and electronic police state thing.

If you are more into the whole, helping people and medical care thing, check out the global consortia at ENIGMA who have been carrying out massive genetic and brain scanning studies – like this one involving 437,607 SNPs in 31,622 voxels in 731 subjects using their new method, vGeneWAS, to study Alzheimer’s Disease:

“We hypothesized that vGeneWAS would, in some situations, have greater power to detect associations than existing SNP-based methods. One such situation might be when a gene contains many loci with weak individual effects. In addition, we expected that vGeneWAS would have greater overall power than mass SNP-based methods, like vGWAS, because of the drastic reduction in the effective number of statistical tests performed.”

The vGeneWAS method relies on the calculation of “eigenSNPs” which are eigenvectors that describe a matrix of n subjects by m SNPs in an individual gene (an n-x-m matrix of 1’s,0’s,-1’s for aa, aA, AA genotypes).  EigenSNPs are sort of like eigenfaces insofar as eigenSNPs (which are not actual SNPs) capture the majority of variance, or the basic essence of an individual gene … but seriously, you should read the original article ’cause every stats test I ever took totally punched me in the face.

In any case, the eigenSNP-by-voxel method pulled out some legit results such as rs2373115 (where the G-allele confers risk) in the GAB2 gene  which has repeatedly been implicated in the risk of age-related late-onset Alzheimer’s Disease (in folks who carry ApoE4  rs429358(C) alleles).  The authors found that the genetic risk of AD conferred by GAB2 may arise by way of GAB2’s effect on brain structure in the periventricular areas, which have been known to be among the first brain regions to show AD-related changes (time-lapse movie of AD tissue loss in the brain).

Picture 2


Genes that confer risk for illness are ideal targets for prevention and treatment.  So, also, are genes associated with natural or treatment-based RECOVERY from illness.  In a search for “recovery genes”, association studies in women who have recovered from eating disorders (ED) vs. those who are still struggling to recover reveals that the C-allele of rs17536211 is associated with recovery.

From Bloss et al.:  “Given the substantial genetic component in the etiology of EDs in general, it follows that there may be genetic variants that contribute to the likelihood of recovery.”

“These were women who were over age 25 years, carried a lifetime diagnosis of either AN, BN, or ED-NOS (ie, subthreshold AN or BN), and for whom data were available regarding the presence (n=361 endorsed ongoing ED symptoms in the past year and considered ‘ill’) or absence (n=115 no ED symptoms in the past year and considered ‘recovered’) of ED symptoms.”

“rs17536211, an intronic SNP in GABRG1 on chromosome 4, showed the strongest statistical evidence of association with a GC-corrected p-value of 4.63 × 10−6, which corresponds to an FDR of 0.021 (Figure 1). The odds ratio (OR) observed for this SNP is 0.46, suggesting that possession of copies of the minor allele [C] is protective from long-term chronic illness (ie, it is associated with recovery).”

How might this SNP confer a protective effect?  The authors review data on the role of GABRG1 subunits in the un-learning of conditioned fear responses [“GABRG1 subunits are found in the lateral inputs, a region that arises from the intercalated cells masses, and is thought to be responsible for mediating inhibition of amygdala output during extinction of conditioned fear (Likhtik et al, 2008)”] and suggest that individuals with the protective C-alleles may be slightly more able to uncouple eating from a very real and debilitating fear response.

*photo credit

This chart from John Hawks shows how brain volume (y-axis) has increased gradually during the past 2 million years of human evolution. brainsize  rs31480 is an interesting SNP because individuals homozygous for the ancestral “C” allele have slightly smaller cranial volumes than TT individuals (well, at least the individuals in this particular study do).  The SNP is located in the IL3 gene which regulates proliferation in a variety of cell types including neural progenitor cells – thus possibly influencing the development of overall brain size.

Personal sidenote – I have a kind of a big head – literally – but 23andMe does not cover rs31480.  So, yeah, that whole mystery remains. 


Let’s be honest.  We are all great liars … to ourselves, and others.  The big blatant lies (I swear I never had sex with Monica Lewinsky) and the little well-meaning lies (No honey, that dress does not make your butt look big) and especially the lies that contain just enough truth as to seem believable on a global scale (Lowering taxes on the rich will spur economic growth) … are what make our lives, and daytime TV, so interesting.

Pity the poor human brain … for some people think that IT cannot tell a lie. Scientists in collaboration with law enforcement have been measuring the  P300 brain wave  as a sort of lie detector (here, here, here) more specifically  “an accurate, and countermeasure (CM)-resistant P300-based Guilty Knowledge Test.”

Interestingly, the properties of the P300 neural biomarker are highly heritable and associated with a variety of genetic polymorphisms – including rs521674 located in the noradrenergic receptor ADRA2A gene (functions in the alerting and stress response elicited when lying/trying not to lie).

I’m an AT heterozygote at rs521674 and proud of my pro-deceitful suppressed P300 … because sometimes all you have to cling to are the lies you tell yourself.


We all have social networks.  Your friends and family are a network of relationships.  The neural networks in your brain that carry out computations involved in social interactions are another type of “social network”.  These two networks are obviously related – in so far as your ability to self-reference and understand your own internal thoughts and feelings predicts how well you can understand and predict the internal thoughts and feelings of others – and thus how extensive your network of friends and family is likely to be.  The structure of your brain networks may even be related to how many friends you have on facebook.

According to Lencz and colleagues, there is a genetic association between the T-allele of rs1344706 and the structure and connectivity of the neural networks that carry out self-referential processing in the brain … in the so-called “default mode network” that is associated with “stimulus independent” mental activity and with social cognition such as when you are attributing mental states to others.

Interestingly, the T-allele of this SNP – residing in the zinc finger protein 804A gene – has been previously associated with schizophrenia (SZ).

From Lencz and colleagues:

“To our knowledge, this is also the first study to identify a genetic correlate of multiple brain regional GM volumes comprising the default mode network.”

The default mode network comprises regions that show synchronized activity at ‘resting’ baseline, in the absence of specific stimulation (Raichle et al, 2001). Ongoing work has implicated this network in the development of self-referential thought (Spreng and Grady, 2010), which has been specifically implicated in the developmental psychopathology of SZ (Nelson et al, 2009).


[link to research article on loss-of-function variants in the human genome]

Never … except when it’s about male pattern baldness.

Just so you know, neither of you are in charge … so please stop acting like hyper oxygen sensitive drama queens with self-absorbed Lewy body issues when it’s not even really about either of you.  I realize that you both have to work in a toxic stew of lethal reactive oxygen species to pump out limitless quantities of ATP and then die in a shallow, unmarked DNA repair enzyme complex … all so I can lay around and watch The Jerry Springer Show.  I get it.  You are under appreciated.  Listen, if you two would stop sniping at each other on Facebook, I promise I’ll eat more kale, volunteer at a soup kitchen and go to yoga 3 times a week.  Besides, AMP Kinase says that if you don’t get your shit together, he’s going to send mTORC1 over and teach both of you what being “mTORC1-dependent” is all about.

mitochondria and neural health


Hey genome, why U make me stink at networking?

If only there was an allele that LESSENED the apprehensive and uncomfortable feelings I get when meeting new people.

As such negative feelings are the work of my amygdala, I’m wishing for some sort of LOSS-OF-FUNCTION allele that REDUCES the activity of neural circuits involved in the emotional processing of fear … but leaves other neural circuits untouched.

I just want something that takes the edge off new social experiences … yunno?

How about rs33977775 ? It contains a derived (as opposed to ancestral) T-allele that causes a Y135F change that disrupts the binding sites of the NPBWR1 receptor to its neuropeptide ligands (ie. LOSS-OF-FUNCTION).  Amazingly, this receptor has a restricted pattern of gene expression only among limbic circuits involved in emotion and reward processing (ie. EXPRESSED IN EMOTION PROCESSING CIRCUITS ONLY).

In their report, a team of authors measured the reactions of 126 university students to various social stimuli and report that individuals who carry one of these loss-of-function T-alleles (about 30% of the population) show a more positive response to social interactions.

“… the AT group perceived facial expressions more pleasantly than did the AA group, regardless of the category of facial expression. Statistical analysis … also showed that the AT group tended to feel less submissive to an angry face than did the AA group.”

So it seems that rs33977775 may dial down the amygdala response to social stimuli … just enough to ace the job interview, but not so much that you inappropriately hug your new boss. Nice!

Unfortunately, this SNP is not covered by 23andMe v3 and there is no report yet on linkage disequilibrium via 1000 genomes.  Since the frequency of the T-allele is low in African populations (1%) and about 10%-ish in other non-African populations, I guess the odds are that I’m an AA or AT.

As the holidays approach, it’s time to confront the grim reality that is your own personal gene pool.  Forget about your SNP genotypes … as Dr. Francis Collins reminds us to, instead, record a personal family medical history.

… but not like this.  Try openSNP.


Our cells are full of clocks … circadian clocks … whose transcriptional and translational feedback loops at the ancient PER locus oscillate with a period of 24-ish hours … complete with diurnal peaks of vulnerability to cardiac arrest and death.

From the article:  ” … an interesting association with time of death (p = 0.015) in which rs7221412 GG individuals had a mean time of death nearly 7 hours later than rs7221412 AA/AG.”

rs7221412 is not presently covered by 23andMe, but this SNP appears to sit in a haplotype block and is flanked by rs9914077 and rs2585408 … both of which are heterozygous for me … so I guess it’s strictly “carpe diem!” (or at least 7 hours of diem) for me and my AG genotype.

If you’re interested in genomic predictions of this death clock … read more about your telomeres.

Death Clock.org Death Test

Probably not.  The T allele at rs7294919  (“each copy of the T allele was associated with lower hippocampal volume (β=−107.8 mm3, p=2.9×10-11)” )  is very common … like 75%-ish … so, yeah, thanks for my TT genotype Mother Nature … and for yet another part of my body that is, um, small.

Bioinformatical muscles

Colm O’Dushlaine rocked his 23andMe profile … hard! … and then shared it with the world.

Totally. Awesome.


Yesterday was World Diabetes Day.

I almost forgot … which may have something to do with rs6741949.

From the original article:

“… rs6741949 in a DPP4 intron on chromosome 2q24, where the G allele was associated with smaller hippocampal volume (β=−52.8 mm3, p=2.9×10-7).”

The association with DPP4 sheds light on a fascinating connection between diabetes and hippocampal (memory) function.

“Further, DPP4 is an intrinsic membrane glycoprotein and a widely expressed serine exopeptidase. It is also an adipokine over-expressed in visceral adipose tissue of obese persons and those with diabetes, conditions associated with smaller hippocampal volume. A novel class of antidiabetic medications (sitagliptin, and related incretin compounds) inhibits DPP4 to improve insulin sensitivity and glucose tolerance through increased levels of glucagon like proteins-1 and 2 (GLP-1, -2). Interestingly, endogenous incretin GLP-1 is also heavily expressed in some hippocampal neurons and has neuroprotective properties.”


note: 23andMe does not cover rs6741949, but they do cover 2 flanking SNPs that are in pretty good linkage disequilibrium with rs6741949 … so, um, I’m trying to figure out how I might impute/infer my genotype here … hmmm.

rs3788979 (bp162900889) CC D’=0.81 strand + forward
rs6741949 (bp162910223) A?G?              strand + forward
rs4664446 (bp162910403) AG D’=0.86 strand + forward

rs2237717 & rs1130233

Are you good at reading faces?  You can test yourself  (here, here, here) or just get off the interwebz and go talk to a real person.

The MET and the AKT genes encode proteins that are involved in early brain development and in the production of new synapses.  Since reading faces requires a lifetime of trial-and-error learning (ie. making new synaptic connections), these genes would likely support the development of facial recognition skills.

From the original article:  “When the individuals who were [MET/AKT rs2237717/rs1130233] C carrier and G carrier simultaneously were used as the reference group, their facial emotion perception was better than that of those with TT/AA  (p=0.015).”

I’m a MET/AKT rs2237717/rs1130233 CC/GG and, as my genome predicts,  a pretty good face reader … but am not sure if this is a good thing.  Why are you looking at me like that?


“I know it now … that I am here to love her. I love her I love her I love her and she doesn’t even have to tell me she loves me back. That’s how much I love her.”

“There there. Just breathe. I wish you would stop obsessing about everything. This week it is Selena Gomez and last week it was Leela from Futurama. You really need to integrate your everyday thoughts and feelings separately from your fantasy life otherwise people are going to ostracize you.”

“I love ostriches so much.”

“Listen. Stop browsing 23andMe data. Just because the “C” allele at rs25532 increases the transcriptional efficiency of the serotonin transporter does not mean that being an LPR “long/long”, rs25532 “C/C” gives you a license to act obsessively. I mean, you’re a TIGER! You don’t even have those alleles.”

“She’s just so beautiful. I want to scratch your eyes out.”

rs53576 AA (not GG)

I’m so lonely sometimes, but I never want to go out. I have 2 “A” alleles at rs53576 (link to science).

A stable relationship with a nice loyal guy AND a secret wild fling with a swarthy promiscuous guy?  Admit it … you’ve probably been there, done that.

From: Associations between Dopamine D4 Receptor Gene Variation with Both Infidelity and Sexual Promiscuity

“Worldwide median rates of non-paternity, or the rate of men raising children under the pretense of biological parentage, have been suggested to near 9%, or 10% more popularly.”

If the 3rd exon in your dopamine D4 receptor (DRD4) gene carries 7-repeats of a 48-nucleotide sequence (48bp VNTR), then you may be slightly more like Snookie and her booze-addled kooka than you wish to admit.

“The dopaminergic reward pathway influences physiological arousal, pleasure, and intrinsic reward. Humans that possess at least one allele 7-repeats or longer (7R+) display behavioral phenotypes associated with attention deficit hyperactivity disorder (ADHD), alcoholism, financial risk-taking, disinhibition and impulsivity, and sexual behavior.”

But don’t blame it all on your genes.  Your environment can modulate your genetic proclivities.

“In r-selected environments (i.e., unpredictable and unstable environments, where the ability to mate more and produce more offspring is favored), 7R+ genotype would be expected to rise in frequency. That is, in environments where “cad” behavior is adaptive, selective pressure for 7R+ would be positive; but in environments where “dad” behavior is adaptive, selective pressure for 7R+ would be negative. This is consistent with the dramatic differences in DRD4 VNTR allele frequencies and behavioral patterns found globally such as in the generally polygamous and agonistic Yanomamö Indians of South America (high 7R+ frequencies) and the generally egalitarian !Kung of the Kalahari (low 7R+ frequencies).”

I’m a DRD4 double fist pumping 7R/7R … so, like, I guess … that explains a lot of the skeletons in my closet.

Yes, we are all turduckens … or as the scientists formally say, the result of an ancient endosymbiosis.  And yes, if you like the individual flavors of mitochondrial genomes and/or nuclear genomes, you will enjoy the flavor of eukaryotic genomes.  And no, “Baturducken,” is not when each stage of the turducken is wrapped in bats … just bacon.