Chronic pain causes epigenetic changes in the brain and immune system

This 2015 Canadian rodent study by McGill researchers found:

“The critical involvement of DNA methylation in chronic pain. We show that in the PFC [prefrontal cortex], a brain region strongly implicated in chronic pain, a stunning number of promoters [control gene expression] are differentially methylated 9 months after injury. These changes are distant both in time and space from the original injury.

The changes in DNA methylation are highly organized in functional pathways that have been implicated in pain such as dysregulation of dopaminergic, glutamatergic, opioid and serotoninergic systems and important signaling and inflammatory pathways.

Genome-wide DNA methylation modifications of T cells [circulating white blood cells that control immune response] are also associated with nerve injury.

Most of the promoters (72%) identified as differentially methylated in T cells after nerve injury were also affected in the brain. While the methylation profiles in some of these modules were affected in the same direction in the brain and the T cells, others went in opposite direction. This is consistent with the idea that the brain and the immune system play different roles in chronic pain.

These data suggest that:

  • Persistent pain is associated with broad and highly organized organism-wide changes in DNA methylation, including two critical biological systems: the central nervous and immune systems.
  • This work also provides a possible mechanistic explanation for commonly observed comorbidities observed in chronic pain (i.e anxiety, depression).
  • Finally, the sheer magnitude of the impact of chronic pain, particularly in the prefrontal cortex, illustrates the profound impact that living with chronic pain exerts on an individual.”

The news coverage focused on how the study’s findings may lead to non-invasive DNA methylation measurements of chronic pain as well as treatments of the effects. I’d argue that the researchers’ concluding statement of the Discussion section deserved the most focus:

“Beyond the example of chronic pain, the robust and highly organized DNA methylation changes seen here in response to nerve injury provides some of the strongest evidence to date that experience effects DNA methylation landscapes at large distances in time and space.”

The study provided “some of the strongest evidence to date” that experiences caused widespread, long-lasting epigenetic changes. Given experiences’ etiologic functions, research with working hypotheses that experiences may also reverse epigenetic changes should be green-lighted.

“DNA methylation landscapes at large distances in time and space” warrant systematic examination of how experiential epigenetic changes during early life may be reversed by experiential therapies later in life. In the current year, there’s sufficient evidence for modifying research goals to primarily address causes, not just effects.

http://www.nature.com/articles/srep19615 “Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells”

Outward expressions of inner truth

“Truth needs no defense except when that truth is more than the system can integrate; then it requires defenses.

Our merciful brain has found back-up ways to protect us. It keeps the truth from us even when we go on searching for the truth.

After patients have deep feelings they come up with many truths about their lives. It is buried and defended along with the pain. Thus no one has to give anyone insights; they are already there just waiting for the exit.”

http://cigognenews.blogspot.com/2016/01/the-act-out-and-more_29.html “The Act-out and More”

Epigenetics research that was designed to fall one step short of wonderful

This 2015 Edinburgh rodent study found:

“In utero exposure of rats to the analgesics indomethacin or acetaminophen, both of which target PG [prostaglandin] pathways, alters fetal germ cell number and development in both male and female fetuses. This results in modest but detrimental effects on F1 [children] female, but not F1 male, fertility in adulthood.

Fetal (F1) exposure of rats to either analgesic resulted in an effect in the second generation (F2 grand-daughters) that manifested as reduced ovarian size and markedly reduced follicle number in females but with evidence of increased follicle activation. The impact on F2 fertility (which was not studied) is unclear.

Our analgesic exposure regimen coincided with the period of chromatin/epigenetic remodelling of the (F1) fetal germ cells in both sexes, events which also occur in the human in the first trimester of pregnancy. The analgesic effects on F2 ovaries were transmitted via both paternal and maternal F1 lines.”

The limitations section showed that the rodents’ acetaminophen dosage was equivalent to a human overdose:

“We administered only a single dose of analgesics. The dose of acetaminophen which we used, resulted in blood levels of acetaminophen 2.5- to 8-fold higher than the levels reported in humans after normal therapeutic dosing (~60 mg/kg/day, divided into 4 doses) during pregnancy.”


I’m puzzled that the researchers didn’t take one more step, and design a great study. They knew what the additional effort would be, per statements such as:

“The impact on F2 fertility (which was not studied) is unclear.

The analgesic-induced reduction in fetal ovarian germ cell number was of particular concern, as the lifetime complement of oocytes is formed in utero at/around the time of birth in women and rodents.”

F3 great-grandchildren were needed to demonstrate “the impact on F2 fertility.” Testing of F3 great-grandchildren may have also provided evidence for or against transgenerational epigenetic inheritance, because those subjects’ cells would have had no direct exposure effects from analgesics.

Weren’t the researchers at the MRC Centre for Reproductive Health, The Queen’s Medical Research Institute University of Edinburgh, interested in understanding whether or not a pregnant woman who overdosed during her fetus’ early development on an analgesic available to billions of people, could potentially adversely affect not only her (F0) and her children’s (F1) and grandchildren’s (F2) reproductive health, but also her F3 great-grandchildren?

Weren’t the researchers interested in being a part of a great study, one that may have advanced science, one that may have shown whether or not epigenetic information was transmitted between generations in the absence of continued analgesic exposure?

http://www.nature.com/articles/srep19789 “Analgesic exposure in pregnant rats affects fetal germ cell development with inter-generational reproductive consequences”

Epigenetic memories of stress as therapeutic targets

This 2015 Swedish rodent study found:

Histone modifications induced by glucose are associated with activation of TXNIP gene [a proinflammatory gene involved in diabetic kidney disease] transcription.

Glucose-stimulated TXNIP gene expression can be

  • reversed by inhibition of histone acetyltransferase (HAT), or
  • enhanced by inhibition of histone deacetylase (HDAC).”

A 2016 Japanese commentary expounded on the study:

“Epigenetic changes accumulate as cell memory, and this epigenetic memory plays a crucial role in the long-term consequences of adult-onset diseases and aging.

The first stimulus, which might be high glucose levels or hypoxia, changes the condition of histone modification or chromosomal conformations. The changes are then memorized as epigenetic memory in the cells, which could help to maintain epigenetic status in response to the first stimulus.

Consequently, when a second stimulus occurs, cells with epigenetic memory respond to the stimulus promptly by the upregulation of downstream genes through binding transcriptional factors. The cells without epigenetic memory take longer to upregulate the expression of downstream target genes.

High glucose levels that are sustained for long periods appear to change histone modification, resulting in the prompt response of TXNIP gene upregulation. Considering that TXNIP is an important proinflammatory gene, this prompt response increases the likelihood of diabetic complications. TXNIP is reported to be augmented by high glucose levels and to promote oxidative stress.”

The study and commentary provided specific examples of the wide-ranging forms of physiological memory induced by stress.

http://www.sciencedirect.com/science/article/pii/S0085253815000927 “Epigenetic regulation of the thioredoxin-interacting protein (TXNIP) gene by hyperglycemia in kidney”

Confusion may be misinterpreted as altruism and prosocial behavior

This 2015 Oxford human study of altruism found:

“Division of people into distinct social types relies on the assumption that an individual’s decisions in public-goods games can be used to accurately measure their social preferences. Specifically, that greater contributions to the cooperative project in the game reflect a greater valuing of the welfare of others, termed “prosociality.”

Individuals behave in the same way, irrespective of whether they are playing computers or humans, even when controlling for beliefs. Therefore, the previously observed differences in human behavior do not need to be explained by variation in the extent to which individuals care about fairness or the welfare of others.

Conditional cooperators, who approximately match the contributions of their groupmates, misunderstand the game. Answering the standard control questions correctly does not guarantee understanding.

We find no evidence that there is a subpopulation of players that understand the game and have prosocial motives toward human players.

These results cast doubt on certain experimental methods and demonstrate that a common assumption in behavioral economics experiments, that choices reveal motivations, will not necessarily hold.

When attempting to measure social behaviors, it is not sufficient to merely record decisions with behavioral consequences and then infer social preferences. One also needs to manipulate these consequences to test whether this affects the behavior.”

The researchers are evolutionary biologists who had made similar points in previous studies. They addressed possible confounders in the study and supporting information, and provided complete details in the appendix. For example, regarding reciprocity:

“Communication was forbidden, and we provided no feedback on earnings or the behavior of groupmates. This design prevents signaling, reciprocity, and learning and therefore minimizes any order effects.

It might also be argued that people playing with computers cannot help behaving as if they were playing with humans. Such ingraining of behavior would suggest a major problem for the way in which economic games have been used to measure social preferences. In particular, behavior would reflect everyday expectations from the real world, such as reputation concerns or the possibility of reciprocity, rather than the setup of the game and the true consequences of choices.”


Some of the news coverage missed the lead point of how:

“Economic experiments are often used to study if humans altruistically value the welfare of others.

These results cast doubt on certain experimental methods and demonstrate that a common assumption in behavioral economics experiments, that choices reveal motivations, will not necessarily hold.”

Here are several expressions of beliefs in one news coverage article where the author attempted to flip the discussion to cast doubt on the study. It was along the lines of “There’s something wrong with this study (that I haven’t thoroughly read) because [insert aspersion about sample size, etc.]” What motivates such reflexive behavior?


This study should inform social behavior studies that draw conclusions from flawed experimental designs. For example, both:

based their findings on a video game of popping balloons. Neither study properly interpreted their subjects’ decisions per the current study’s recommendation:

“When attempting to measure social behaviors, it is not sufficient to merely record decisions with behavioral consequences and then infer social preferences. One also needs to manipulate these consequences to test whether this affects the behavior.”

http://www.pnas.org/content/113/5/1291.full “Conditional cooperation and confusion in public-goods experiments”


This post has somehow become a target for spammers, and I’ve disabled comments. Readers can comment on other posts and indicate that they want their comment to apply here, and I’ll re-enable comments.

Lifelong effects of stress

A 2016 commentary A trilogy of glucocorticoid receptor actions that included two 2015 French rodent studies started out:

Glucocorticoids (GCs) belong to a class of endogenous, stress-stimulated steroid hormones. They have wide ranging physiologic effects capable of impacting metabolism, immunity, development, stress, cognition, and arousal.

GCs exert their cellular effects by binding to the GC receptor (GR), one of a 48-member (in humans) nuclear receptor superfamily of ligand-activated transcription factors.”

The French studies were exceedingly technical. The first GR SUMOylation and formation of an SUMO-SMRT/NCoR1-HDAC3 repressing complex is mandatory for GC-induced IR nGRE-mediated transrepression:

“GCs acting through binding to the GR are peripheral effectors of circadian and stress-related homeostatic functions fundamental for survival.

Unveils, at the molecular level, the mechanisms that underlie the GC-induced GR direct transrepression function mediated by the evolutionary conserved inverted repeated negative response element. This knowledge paves the way to the elucidation of the functions of the GR at the submolecular levels and to the future educated design and screening of drugs, which could be devoid of undesirable debilitating effects on prolonged GC therapy.”

The companion study Glucocorticoid-induced tethered transrepression requires SUMOylation of GR and formation of a SUMO-SMRT/NCoR1-HDAC3 repressing complex stated:

“GCs have been widely used to combat inflammatory and allergic disorders. However, multiple severe undesirable side effects associated with long-term GC treatments, as well as induction of glucocorticoid resistance associated with such treatments, limit their therapeutic usefulness.”

Even when researchers study causes, they often justify their efforts in terms of outcomes that address effects. Is an etiologic advancement in science somehow unsatisfactory in and of itself?


Once in a while I get a series of personal revelations while reading scientific publications. Paradoxically, understanding aspects of myself has seldom been sufficient to address historical problems.

Thoughts are only where some of the effects of problems show up, and clarifying my understanding can – at most – tamp down these effects. The causes are elsewhere, and addressing them at the source is what ultimately needs to happen.

A few glucocorticoid-related items to ponder:

  • How has stress impacted my life? When and where did it start?
  • Why do I feel wonderful after taking prednisone or other anti-inflammatories? What may be the originating causes of such effects?
  • Why have prolonged periods of my life been characterized by muted responses to stress? How did I get that way?
  • Have I really understood why I’ve reflexively put myself into stressful situations? What will break me out of that habit?
  • Why do the feelings I experience while under stressful situations feel familiar? Does my unconsciousness of their origins have something to do with “homeostatic functions fundamental for survival?”
  • Why haven’t I noticed that symptoms of stress keep showing up in my life? There are “physiologic effects capable of impacting metabolism, immunity,” etc. but I don’t do something about it?
  • How else may stress impact my biology? Brain functioning? Ideas and beliefs? Behavior?

The purpose of many epigenetic processes is to control virus-like material

This 2016 Swiss human review’s subject was:

“Transposable elements (TEs) may account for up to two-thirds of the human genome, and as genomic threats they are subjected to epigenetic control mechanisms engaged from the earliest stages of embryonic development.

TEs are present in all organisms from bacteria to humans, and they constitute essential motors of evolution. TEs are phylogenetically and biologically related to viruses.

TEs can disrupt genes, provide novel coding activities, exert a wide range of transcriptional influences, and, because of their repetitive nature, create grounds for recombination events leading to genomic deletions and duplications, yet only a very small minority of TEs present in the human genome are still transposition-competent, accounting for one new germline integrant in 20 to 50 human births, and none is capable of horizontal transfer.

A vast majority of these DNA-binding proteins, including many of those expressed in human differentiated cells, primarily recognize sequences contained within TEs..controlling the transcriptional potential of their TE targets well beyond the early embryonic period..modulating the transcriptional impact of TE-residing sequences that are co-opted to regulate the expression of cellular genes.

A large fraction of the recognizable mobile elements in our genome are unique to humans or close relatives. The impact of this phenomenon on speciation might be particularly pronounced in organs subjected to environmental constraints that are not overly coercive, such as the brain..the central nervous system.”

The author presented evidence that the purpose of many ongoing epigenetic processes is to silence or otherwise “tame” TEs “to regulate the expression of cellular genes.” The author contrasted his view with the view that:

“Beyond this early embryonic period, TEs become permanently silenced, and that the evolutionary selection of TE controllers is the result of a simple evolutionary arms race between the host and these genetics invaders.”

http://symposium.cshlp.org/content/early/2016/01/13/sqb.2015.80.027573.long “Transposable Elements, Polydactyl Proteins, and the Genesis of Human-Specific Transcription Networks”

State-dependent brain functions and adrenaline

This 2015 German/Italian rodent study investigated:

“How a specific neuromodulatory input may influence the information content and the readout of cortical information representations of sensory stimuli.

The locus coeruleus (LC) is a brainstem neuromodulatory nucleus that likely plays a prominent role in shaping cortical states via a highly distributed noradrenaline release in the forebrain. In particular, the LC:

  • Contributes to regulation of arousal and sleep;
  • Is involved in cognitive functions such as vigilance, attention, and selective sensory processing; and
  • Modulates cortical sensory responses and cortical excitability.

An important addition of our work to previous models of state dependence was the inclusion of the contribution of an important neuromodulator – the noradrenergic system. Our results support the hypothesis that the temporal structure of LC firing causally influences cortical dynamics.

Our work highlights the importance of timing of LC burst: suitably timed LC burst (for example, triggered by an alerting stimulus) can very rapidly trigger transitions into excitable cortical states, which in turn decrease the threshold for cortical responses and thus dynamically facilitate the processing of salient or attended events.

State dependence may either:

  • Force neurons to transmit information only using codes that are robust to state fluctuations (e.g., relative firing rates), or may
  • Force downstream neurons to gain information about the state of the networks sending the sensory messages and then to use the knowledge of state to properly interpret neural responses.

Our results suggest that the latter information transmission scheme is feasible, because detecting state by either monitoring the dynamics of cortical ongoing activity alone or by also monitoring the dynamics of noradrenergic modulation substantially increased the amount of information about sensory stimuli in the late response components relevant for behavior.”

The study added to the evidence that state dependencies can’t be overlooked in explanations of brain function and resultant physical and mental activity. Locus coeruleus neural activity “can very rapidly trigger transitions into excitable cortical states..and thus dynamically facilitate the processing of salient or attended events.”

Adrenaline from the locus coeruleus produced a state of arousal in multiple brain and body areas tied into the subjects’ sympathetic nervous systems. Such internal state changes may be accompanied by state-dependent memories, following the findings of What can cause memories that are accessible only when returning to the original brain state?

The study highlighted the capability of a lower brain structure to influence other brain areas. Its findings should inform researchers in attention and behavior studies, especially when investigating causes of attention and behavior difficulties.

http://www.pnas.org/content/112/41/12834.full “Modeling the effect of locus coeruleus firing on cortical state dynamics and single-trial sensory processing”

Treating prenatal stress-related disorders with an oxytocin receptor agonist

This 2015 French/Italian rodent study found:

“Chronic systemic treatment with carbetocin [unavailable in the US] in PRS [prenatally restraint stressed] rats corrected:

  • the defect in glutamate release,
  • anxiety– and depressive-like behavior,

and abnormalities:

  • in social behavior,
  • in the HPA response to stress, and
  • in the expression of stress-related genes in the hippocampus and amygdala.

These findings disclose a novel function of oxytocin receptors in the hippocampus, and encourage the use of oxytocin receptor agonists in the treatment of stress-related psychiatric disorders in adult life.”

carbetocin

The adult male subjects were:

“PRS rats..the offspring of dams exposed to repeated episodes of restraint stress during pregnancy.

These rats display anxiety- and depressive-like behaviors and show an excessive glucocorticoid response to acute stress, which is indicative of a dysregulation of the hypothalamus-pituitary-adrenal (HPA) axis caused by an impaired hippocampal glucocorticoid negative feedback.

PRS rats show a selective reduction in glutamate release in the ventral hippocampus.”

The researchers cited several other studies they have performed with the PRS phenotype. In the current study:

“Carbetocin treatment had no effect on these behavioral and neuroendocrine parameters in prenatally unstressed (control) rats, with the exception of a reduced expression of the oxytocin receptor gene in the amygdala.

Carbetocin displayed a robust therapeutic activity in PRS rats, but had no effect in unstressed rats, therefore discriminating between physiological and pathological conditions.”


The PRS phenotype showed the ease with which a child can be epigenetically changed – even before they’re born – to be less capable over their entire life. Just stress the pregnant mother-to-be.

https://www.sciencedirect.com/science/article/abs/pii/S0306453015002395 “Activation of presynaptic oxytocin receptors enhances glutamate release in the ventral hippocampus of prenatally restraint stressed rats” (not freely available) Thanks to coauthor Dr. Eleonora Gatta for providing the full study.

What was not, is not, and will never be

Neuroskeptic’s blog post Genetic Testing for Autism as an Existential Question related the story of “A Sister, a Father and a Son: Autism, Genetic Testing, and Impossible Decisions.”

“I decided to put the question to my sister, Maria. Although she is autistic, she is of high intelligence.

Maria was excited to be an aunt soon, and was willing to do what she could to help my baby – even if what she was helping with was to avoid her own condition.

She is high enough functioning to know some of what she’s missing in life, and has longed her entire life to be “normal.” If she could save her niece or nephew some of the pain and awkwardness her condition had caused her, she was willing to help.”

In the concluding paragraph:

“What struck me about this story is the way in which the prospect of the genetic test confronted Maria with a very personal decision: will you do something that might help prevent someone else becoming like you?

Isn’t this very close to the ultimate existential question: all things considered, would you wish to live your life over again?”


Aren’t the majority of humans also “high enough functioning to know some of what she’s missing in life?”

Aren’t our feelings of what we’re missing one of the impetuses for us to have also “longed her entire life to be normal?”

This feeling was aired in Dr. Arthur Janov’s blog post What a Waste:

“What it was, was the feeling of great loss, something missing that could never again be duplicated.

It was no love where it could have been the opposite if the parent’s gates could have been open. But it could not be because that would have meant terrible pain and suffering for them; and their whole neurologic system militated against any conscious-awareness.”


We long for what was and is impossible:

  • For many of us, the impossibilities of having normal lives started with prenatal epigenetic changes.
  • Our experiences of our postnatal environment prompted us into adapting to its people, places, and contents. These neurological, biological, and behavioral adaptations were sometimes long-lasting deviations from developmental norms.
  • Other genetic factors combined with the above to largely make us who we were and are.

Our longing for an impossible-to-reconstruct life doesn’t go away.

We often may not be aware of our longing for what “could not be” and of its extensive impacts. Such feelings impel us into many hundreds of ideas, hundreds of beliefs, and hundreds of behaviors, a sample of which were referred to above:

  • Behaviors to “do something that might help prevent someone else becoming like you;”
  • Ideas such as existential philosophy; and
  • Beliefs that manifest the “wish to live your life over again.”

Spending our time on these ideas, beliefs, and behaviors won’t ameliorate their motivating causes. Our efforts distance us from our truths, with real consequences: a wasted life.

What keeps us from understanding our reality? I invite readers to investigate Dr. Arthur Janov’s Primal Therapy for effective therapeutic approaches.

Are hormone ratios useful in explaining health? Behavior? Neurobiology? Anything?

This 2015 Zurich human review addressed:

“A remarkable lack of discussion on the meaning and interpretation of frequently used hormone ratios.

The interpretation of hormone ratios is complicated and in many cases not sufficiently supported from a theoretical point of view.

Based on the assumption that the balance between two interdependent hormones determines their eventual effects on brain and other tissues, this index has been commonly interpreted as an indicator of the balance between two endocrine systems.

The ratio is typically calculated by simply dividing the raw value of one hormone by the raw value of a second hormone. However, endocrine parameters may fluctuate considerably within individuals across short periods of time on the basis of circadian rhythms or contextual factors. Nevertheless, the ratio method has so far only rarely been applied in the context of repeated endocrine assessments.”

The researchers made a non-exhaustive list of three dozen studies that used hormone ratios among cortisol, dehydroepiandrosterone sulfate (DHEA-S), estradiol, progesterone, testosterone, triiodothyronine (T3), thyroxine (T4), etc., to explain various outcome measures such as:

  • “Health status
  • Aggressive behavior
  • Psychopathy
  • Marital violence
  • fMRI response to angry and happy faces
  • Early life adversity
  • Depression
  • Chronic stress
  • Alexithymia”

Their 2015 study on “endocrine correlates of pro-environmental behavior” was used as an illustrative example. It had 229 male subjects between ages 19 and 77. Salivary cortisol (C) and testosterone (T) was sampled with these results:

“T/C and C/T ratios produce different means, standard deviations and distributional properties which significantly deviate from normality.

Height is not significantly associated with either T/C or C/T. In fact, looking at the original variables, C correlates positively with height while T shows no association.

When we include age as a covariate (assuming that it is associated with both height and hormone status) the partial correlation between T/C and height then is significant while the association between C/T and height is non-significant, even though both ratios are based on the exact same data.

Looking at the negative association between age and T/C the observed age-related ratio decline is mainly due to the fact that the T value in the numerator decreases with age while the C value in the denominator remains relatively constant. In this case, the analysis of the individual variables therefore offers more information and a more accurate picture of the underlying relationships.


A few previous studies have standardized the two underlying hormone distributions before calculating the ratio in order to account for the fact that two hormones often exhibit very different means and standard deviations. Standardization leads to values that express each subject’s hormone concentration relative to the sample mean.

A ratio calculated on the basis of such standardized hormones takes on a different meaning. In particular, the ratio no longer merely represents the proportion of the two hormones within the individual but also incorporates how high the two hormone concentrations are with respect to the sample distributions.”


Practices to improve the use and interpretation of hormone measurements included:

“Regression techniques employed on the original variables constitute a better suited alternative devoid of the problems associated with the ratio method. Moderation analysis, in particular, is a useful approach, which often provides more detailed insight into the relationships of interest.

Ratios should either be analyzed with non-parametric techniques, or be log-transformed before parametric statistical methods are applied.”

Set points and variations in an individual’s hormone balances are usually effects of underlying causes. Researchers will hopefully pay more attention to effectively dealing with ultimate causes as the preferred methods of managing an individual’s health, behavioral, and neurobiological effects.

http://www.psyneuen-journal.com/article/S0306-4530%2815%2900953-1/fulltext “How to use and interpret hormone ratios”

Stress consequences on gut bacteria, behavior, immune system, and neurologic function

This 2015 Canadian rodent study found:

“Chronic social defeat induced behavioral changes that were associated with reduced richness and diversity of the gut microbial community.

The degree of deficits in social, but not exploratory behavior was correlated with group differences between the microbial community profile.

Defeated mice also exhibited reduced abundance of pathways involved in the biosynthesis and metabolism of tyrosine and tryptophan: molecules that serve as precursors for the synthesis of dopamine, norepinephrine, serotonin, and melatonin, respectively.

This study indicates that stress-induced disruptions in neurologic function are associated with altered immunoregulatory responses.”

The researchers had an extensive Discussion section where they tied the study’s findings to other rodent and human studies. For example:

“Our analyses also predicted reduced frequency of fatty acid biosynthesis and metabolism pathways, including that of propanoate and butanoate—the byproducts of dietary carbohydrate fermentation by intestinal microorganisms.

Butyrate is a potent histone deacetylase (HDAC) inhibitor that exerts antidepressant-like effects by increasing histone acetylation in the frontal cortex and hippocampus, and consequentially, raising BDNF transcript levels.

Although it was previously unclear whether the systemic levels of these metabolites achieved in vivo were sufficient to produce behavioral changes, progress has been made by discovering their presence in the cerebrospinal fluid and the brain, and demonstrating that colon-derived SCFAs [short chain fatty acids] cross the blood–brain barrier and preferentially accumulate in the hypothalamus, where they can affect CNS activity.”

http://www.psyneuen-journal.com/article/S0306-4530%2815%2900934-8/fulltext “Structural & functional consequences of chronic psychosocial stress on the microbiome & host”

A problematic study of testosterone’s influence on behavior and brain measurements

This 2015 US/Canadian human study of people ages 6 to 22 years found:

“Testosterone-specific associations between amygdala volume and key prefrontal areas involved in emotional regulation and impulse control:

  1. Testosterone-specific modulation of the covariance between the amygdala and medial prefrontal cortex (mPFC);
  2. A significant relationship between amygdala-mPFC covariance and levels of aggression; and
  3. Mediation effects of amygdala-mPFC covariance on the relationship between testosterone and aggression.

These effects were independent of sex, age, pubertal stage, estradiol levels and anxious-depressed symptoms.

For the great majority of individuals in this sample, higher thickness of the mPFC was associated with lower aggression levels at a given amygdala volume. This effect diminished greatly and disappeared at more extreme amygdala values.”

The study provided noncausal associations among the effects (behavioral, hormonal, and brain measurements).


From the Limitations section:

“No umbilical cord or amniotic measurements were available in this study and we therefore cannot control for testosterone levels in utero, a period during which significant testosterone-related changes in brain structure are thought to occur.”

There’s evidence that too much testosterone for a female fetus and too little testosterone for a male fetus both have lifelong adverse effects. The researchers dismissed this etiologic line of inquiry with a “supporting the notion” referral to noncausal studies.


The researchers were keen to establish:

“A very specific, aggression-related structural brain phenotype.”

This putative phenotype hinged on:

  • Older subjects’ behavioral self-reports, and
  • Parental assessments of younger subjects’ behavior

exhibited during the previous six months, and within six months of their fMRI scan.

These self-reports and interested-party observations were the entire bases for the “aggressive behavior” and “anxious–depressed” associations! The researchers disingenuously provided multiple references and models for the reliability of these assessments.


Experimental behavioral measurements – such as those done to measure performance in decision studies – may have been more accurate and informative than what the older subjects chose to self-report about their own behavior over the previous six months.

People of all ages have an imperative to NOT be completely honest about their own behavior. One motivation for this condition is that some of our historical realities are too painful to enter our conscious awareness and inform us about our own behavior. As a result, our feelings, thoughts, and behavior are sometimes driven by our histories without us being aware of it.

For example, would a teenager/young adult subject self-report an impulsive act, even if they didn’t fully understand why they acted that way? Maybe they would if the act could be viewed as prosocial, but what if it was antisocial?

What are the chances that the lives of these teenager/young adult subjects were NOT filled with impulsive actions during the six months before their fMRI scans? Could complete and accurate self-reports of such behaviors be expected?

Experimental behavioral measurements may have also been more accurate and informative than second-hand, interested-party observations of the younger subjects. Could a parent who provided half of the genes and who was responsible for many of their child’s epigenetic changes make anything other than subjective observations of their handiwork’s behavior?


Epigenetic studies have shown that adaptations to environments are among the long-lasting causes for effects that include behavior, hormones, and brain measurements. Why, in 2015, did researchers spend public funds developing what they knew or should have known would be noncausal associations, while not investigating possible causes for these effects?

Why weren’t the researchers interested enough to gather and assess etiologic genetic and epigenetic evidence? Was it that difficult to get blood samples at the same time the subjects gave saliva samples, and perform selected genetic and DNA methylation analyses?

What did the study contribute towards advancing science? Who did the study really help?

My judgment: less than nothing; and nobody. The researchers only wasted public funds advancing a meme, giving it an imprimatur of science.

http://www.psyneuen-journal.com/article/S0306-4530%2815%2900924-5/fulltext “A testosterone-related structural brain phenotype predicts aggressive behavior from childhood to adulthood”

The cerebellum’s role in human behavior and emotions

This 2016 Italian human review considered the lower brain’s contributions to an individual’s behavior and temperament:

“In evidencing associations between personality factors and neurobiological measures, it seems evident that the cerebellum has not been up to now thought as having a key role in personality.

Cerebellar volumes correlate positively with novelty seeking scores and negatively with harm avoidance scores. Subjects who search for new situations as a novelty seeker does (and a harm avoiding does not do) show a different engagement of their cerebellar circuitries in order to rapidly adapt to changing environments.

Cerebellar abilities in planning, controlling, and putting into action the behavior are associated to normal or abnormal personality constructs. In this framework, it is worth reporting that increased cerebellar volumes are even associated with high scores in alexithymia, construct of personality characterized by impairment in cognitive, emotional, and affective processing.”

The full paper wasn’t freely available, but a list of the 173 references was. 17 references were of alexithymia, also mentioned in the title.


One freely available reference was The embodied emotion in cerebellum: a neuroimaging study of alexithymia, a 2014 study performed by these same authors, which found:

“Alexithymia scores were linked directly with cerebellar areas and inversely with limbic and para-limbic system, proposing a possible functional modality for the cerebellar involvement in emotional processing.

The increased volumes in Crus 1 of subjects with high alexithymic traits may be related to an altered embodiment process leading to not-cognitively interpreted emotions.”

“Alexithymia scores” referred to one of the methods used to characterize alexithymia symptoms, self-reported answers to questionnaires such as this one. Sample questions from the questionnaire used by the referenced study are:

  • “I am often confused about what emotion I am feeling
  • It is difficult for me to reveal my innermost feelings, even to close friends”

The questionnaire mainly engages a person’s cerebrum. The person may recall emotions, and form ideas as framed by each question. Then they’ll describe these ideas in terms of a scaled answer.

Cerebral answers may provide historical contexts for feelings. However, the person’s cerebellum and other brain areas aren’t necessarily engaged by the diagnostic questionnaire.

Without this engagement, the person may not experience feelings when providing answers about feelings. The answers may be more along the lines of “This is what I think I should be feeling” or “This is what I think I should tell the researchers about what I think I should feel.”


  • Can a questionnaire accurately determine associations among engaged and unengaged brain areas?
  • What can be done regarding “impairment in cognitive, emotional, and affective processing?”
  • What’s the lower brain’s “involvement in emotional processing?”
  • How does the lower brain shape a person’s behavior and traits?
  • When and where in an individual’s lifespan does their cerebellum develop?

http://link.springer.com/article/10.1007/s12311-015-0754-9 “Viewing the Personality Traits Through a Cerebellar Lens: a Focus on the Constructs of Novelty Seeking, Harm Avoidance, and Alexithymia”

Testing the null hypothesis of oxytocin’s effects in humans

“There are so many reports of relationships between oxytocin and social behaviors. It is impossible that not a single one of these effects is real.

Isn’t it?

When running a battery of three tasks for every subject who underwent oxytocin treatment..finding false effects becomes almost guaranteed – over 90%.”

http://theneuroeconomist.com/2016/01/the-self-justification-molecule-how-have-we-accumulated-a-vast-behavioral-oxytocin-literature-for-over-a-decade/ “The self-justification molecule: how have we accumulated a vast behavioral oxytocin literature for over a decade”


From one of the references, Why Most Published Research Findings Are False:

“For many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias.”


Also see the researcher’s response on their blog post Does oxytocin increase trust in humans? Frequently asked questions:

“Scientists publish only positive findings and not negative ones, and I cannot think of a single study in the vast human oxytocin literature that was replicated by an independent research group.”