Going off the rails with the biomarker paradigm

This 2018 US government rodent study used extreme dosages to achieve its directed goals of demonizing nicotine and extolling the biomarker paradigm:

“This study examined whether adolescent nicotine exposure alters adult hippocampus-dependent learning, involving persistent changes in hippocampal DNA methylation and if choline, a dietary methyl donor, would reverse and mitigate these alterations.

Mice were chronically treated with nicotine (12.6mg/kg/day) starting at post-natal day 23 (pre-adolescent), p38 (late adolescent), or p54 (adult) for 12 days followed by a 30-day period during which they consumed either standard chow or chow supplemented with choline (9g/kg).

Our gene expression analyses support this model and point to two particular genes involved in chromatin remodeling, Smarca2 and Bahcc1. Both Smarca2 and Bahcc1 showed a similar inverse correlation pattern between promoter methylation and gene expression.

Our findings support a role for epigenetic modification of hippocampal chromatin remodeling genes in long-term learning deficits induced by adolescent nicotine and their amelioration by dietary choline supplementation.”


Let’s use the average weight of a US adult male, which is published by the US Centers for Disease Control at 88.8 kg, to compare dosages:

  1. Nicotine at “12.6mg/kg/day” x 88.8 = 1119 mg, The estimated lower limit of a lethal dose of nicotine has been reported as between 500 and 1000 mg!
  2. Choline at “9g/kg” x 88.8 = 799 g. The US National Institutes of Health published the Tolerable Upper Intake Levels for Choline as 3.5 g!

A funding source of this study was National Institute on Drug Abuse (NIDA) Identification of Biomarkers for Nicotine Addiction award (T-DA-1002 MG). Is the biomarker paradigm institutionalized to the point where studies that don’t have biomarkers as goals aren’t funded?

Is the main purpose of animal studies to help humans? Or is it to promote an agenda?

https://www.sciencedirect.com/science/article/pii/S107474271830193X “Choline ameliorates adult learning deficits and reverses epigenetic modification of chromatin remodeling factors related to adolescent nicotine exposure” (not freely available)

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A book review of “Neuroepigenetics and Mental Illness”

A 2018 online book “Neuroepigenetics and Mental Illness” was published at https://www.sciencedirect.com/bookseries/progress-in-molecular-biology-and-translational-science/vol/158/suppl/C (not freely available). Three chapters are reviewed here, with an emphasis on human studies.

“Chapter Five: Neuroepigenetics of Prenatal Psychological Stress” https://www.sciencedirect.com/science/article/pii/S1877117318300747 (not freely available)

“Chapter Eleven: Using Epigenetic Tools to Investigate Antidepressant Response” https://www.sciencedirect.com/science/article/pii/S1877117318300711 (not freely available)

“Chapter Twelve: Transgenerational Epigenetics of Traumatic Stress” https://www.sciencedirect.com/science/article/pii/S187711731830053X (not freely available)


Actually, I won’t waste my time or your time with what I planned to do. The lack of scientific integrity and ethics displayed by the book’s publisher, editor, and contributors in the below chapter spoke volumes.

How can the information in any other chapter of this book be trusted?


“Chapter Twelve: Transgenerational Epigenetics of Traumatic Stress”

This chapter continued propagating a transgenerational meme that had more to do with extending paradigms than science. The meme is that there are adequately evidenced transgenerational epigenetic inheritance human results.

As I most recently noted in Epigenetic variations in metabolism, there aren’t any published human studies that provide incontrovertible evidence from the F0 great-grandparents, F1 grandparents, F2 parents, and F3 children to confirm definitive transgenerational epigenetic inheritance causes and effects. Researchers urgently need to do this human research, and stop pretending it’s already done.

How did the book’s editor overlook what this chapter admitted?

“Literature about the inheritance of the effects of traumatic stress in humans has slowly accumulated in the past decade. However, it remains thin and studies in humans also generally lack clear “cause and effect” association, mechanistic explanations or germline assessment.”

Were the publisher and editor determined to keep the chapter heading and the reviewers determined to add another entry to their CVs in the face of this weasel-wording?

“In conclusion, although less studied from a mechanistic point of view, inter- and possibly transgenerational inheritance of the effects of traumatic stress is supported by empirical evidence in humans.”

See the comments below for an example of the poor substitutes for evidence that propagators of the transgenerational meme use to pronounce human transgenerational epigenetic inheritance a fait accompli.

A disturbance in the paradigm of child abuse

The principal way science advances is through the principle Einstein expressed as:

“No amount of experimentation can ever prove me right; a single experiment can prove me wrong.”

Members of the scientific community and of the public should be satisfied that the scientific process is working well when hypotheses are discarded due to nonconfirming evidence. Researchers should strive to develop evidence that rejects paradigms, and be lauded for their efforts.

The opposite took place with this 2018 commentary on two studies where the evidence didn’t confirm current biases. I curated one of these studies in DNA methylation and childhood adversity.

The commentators’ dismissive tone was set in the opening paragraph:

“Is early exposure to adversity associated with a genetic or an epigenetic signature? At first glance, two articles in this issue -..and the other from Marzi et al., who measured genome-wide DNA methylation in a prospective twin cohort assessed at age 18 – appear to say that it is not.”

The two commentators, one of whom was a coauthor of Manufacturing PTSD evidence with machine learning, went on to protect their territory. Never mind the two studies’ advancement of science that didn’t coincide with the commentators’ vested interests.


My main concern with the study was that although the children had been studied at ages 5, 7, 10, 12, and 18, the parents had never been similarly evaluated! The researchers passed up an opportunity to develop the parents as a F0 generation for understanding possible human transgenerational inherited epigenetic causes and effects.

The study focused on the children’s intergenerational epigenetic effects. However, animal studies have often demonstrated transgenerational effects that skip over the F1 generation children!

For example:

https://ajp.psychiatryonline.org/doi/pdf/10.1176/appi.ajp.2018.18020156 “Considering the Genetic and Epigenetic Signature of Early Adversity Within a Biopsychosocial Framework” (not freely available)

How to hijack science: Ignore its intent and focus on the 0.0001%

This 2018 Belgian review hijacked science to further an agenda:

“We addressed this issue at the LATSIS Symposium ‘Transgenerational Epigenetic Inheritance: Impact for Biology and Society’, in Zürich, 28–30 August 2017, and here provide important arguments why environmental and lifestyle-related exposures in young men should be studied.”

The reviewer DETRACTED from science in the studied area – transgenerational epigenetic inheritance – by ignoring its intent. As shown by A self-referencing study of transgenerational epigenetic inheritance which I also curated today, the purpose of such animal studies is to find the mechanisms in order to help humans.


Putting that study’s graphic into human terms, F3 male great-grandchildren may be adversely affected by their F0 great-grandmothers being poisoned while pregnant with their F1 grandfathers, who – with their F2 fathers – may have also been adversely affected.


What the reviewer asserted without proof:

“The importance of maternal lifestyle, diet and other environmental exposures before and during gestation period is well recognized.”

is NOT TRUE for the studied area.

The evidence disproving this assertion is that NO HUMAN STUDIES scientifically demonstrating causes for transgenerational epigenetic inheritance effects have been published!

EVER!!

There’s a huge gap between “The importance..is well recognized” of anything regarding transgenerational epigenetic inheritance and ZERO human studies.

Why has no one published scientifically adequate human evidence to demonstrate “Transgenerational Epigenetic Inheritance: Impact for Biology and Society” effects on ALL of the F1, F2, and F3 human generations as consequences “of maternal lifestyle, diet and other environmental exposures before and during gestation period?” What are we waiting for?

The reviewer said “young men should be studied” but said nothing about resolving bottlenecks in funding human research of the studied area. Do researchers even have opportunities to make a NON-AGENDA-DRIVEN difference in this field?

With ZERO published human studies, transgenerational epigenetic inheritance research can’t be recharacterized into a female vs. male agenda. The reviewer’s attempt to do so diminished the importance of research into human critical development periods.

This agenda’s viewpoint ignored human correlates of evidence from animal studies like The lifelong impact of maternal postpartum behavior:

“The defect in maternal care induced by gestational stress programs the development of the offspring.”

Will the reviewer’s suggested interventions – such as changing an adult’s lifestyle a long time after their development was altered – somehow make up for what went wrong early in their life, even before they were born?

With the evidence from animal studies such as:

is there any doubt that similar mechanisms may be involved in humans, and that human phenotypes may likewise be intergenerationally and/or transgenerationally transmitted?

The reviewer asserted:

“Studying humans is challenging, because of ethical reasons”

But do “ethical reasons” prohibit non-instigating human studies of stress, the intergenerationally and transgenerationally transmitted effects of which seem to be ubiquitous among humans?

In The Not-Invented-Here syndrome I pointed out another problem that the reviewer’s agenda is less than helpful in resolving:

“How can animal studies like the current study help humans when their models don’t replicate common human conditions? This failure to use more relevant models has follow-on effects such as human intergenerational and transgenerational epigenetic inheritance being denigrated due to insufficient evidence.”


I’ll repeat What is a father’s role in epigenetic inheritance? in closing:

“The review focused on 0.0001% of the prenatal period for what matters with the human male – who he was at the time of a Saturday night drunken copulation – regarding intergenerational and transgenerational epigenetic inheritance of metabolic diseases.

The human female’s role – who she was at conception AND THEN what she does or doesn’t do during the remaining 99.9999% of the prenatal period to accommodate the fetus and prevent further adverse epigenetic effects from being intergenerationally and transgenerationally transmitted – wasn’t discussed.

Who benefits from this agenda’s narrow focus?”

https://academic.oup.com/eep/article/4/2/dvy007/4987171 “POHaD: why we should study future fathers”

Resiliency in stress responses

This 2018 US Veterans Administration review subject was resiliency and stress responses:

Neurobiological and behavioral responses to stress are highly variable. Exposure to a similar stressor can lead to heterogeneous outcomes — manifesting psychopathology in one individual, but having minimal effect, or even enhancing resilience, in another.

We highlight aspects of stress response modulation related to early life development and epigenetics, selected neurobiological and neurochemical systems, and a number of emotional, cognitive, psychosocial, and behavioral factors important in resilience.”

The review cited studies I’ve previously curated:


There were two things I didn’t understand about this review. The first was why the paper isn’t freely available. It’s completely paid for by the US taxpayer, and no copyright is claimed. I recommend contacting the authors for a copy.

The second was why the VA hasn’t participated in either animal or human follow-on studies to the 2015 Northwestern University GABAergic mechanisms regulated by miR-33 encode state-dependent fear. That study’s relevance to PTSD, this review’s subject, and the VA’s mission is too important to ignore. For example:

“Fear-inducing memories can be state dependent, meaning that they can best be retrieved if the brain states at encoding and retrieval are similar.

“It’s difficult for therapists to help these patients,” Radulovic said, “because the patients themselves can’t remember their traumatic experiences that are the root cause of their symptoms.”

The findings imply that in response to traumatic stress, some individuals, instead of activating the glutamate system to store memories, activate the extra-synaptic GABA system and form inaccessible traumatic memories.”

I curated the research in A study that provided evidence for basic principles of Primal Therapy. These researchers have published several papers since then. Here are the abstracts from three of them:

Experimental Methods for Functional Studies of microRNAs in Animal Models of Psychiatric Disorders

“Pharmacological treatments for psychiatric illnesses are often unsuccessful. This is largely due to the poor understanding of the molecular mechanisms underlying these disorders. We are particularly interested in elucidating the mechanism of affective disorders rooted in traumatic experiences.

To date, the research of mental disorders in general has focused on the causal role of individual genes and proteins, an approach that is inconsistent with the proposed polygenetic nature of these disorders. We recently took an alternative direction, by establishing the role of miRNAs in the coding of stress-related, fear-provoking memories.

Here we describe in detail our work on the role of miR-33 in state-dependent learning, a process implicated in dissociative amnesia, wherein memories formed in a certain brain state can best be retrieved if the brain is in the same state. We present the specific experimental approaches we apply to study the role of miRNAs in this model and demonstrate that miR-33 regulates the susceptibility to state-dependent learning induced by inhibitory neurotransmission.”

Neurobiological mechanisms of state-dependent learning

“State-dependent learning (SDL) is a phenomenon relating to information storage and retrieval restricted to discrete states. While extensively studied using psychopharmacological approaches, SDL has not been subjected to rigorous neuroscientific study.

Here we present an overview of approaches historically used to induce SDL, and highlight some of the known neurobiological mechanisms, in particular those related to inhibitory neurotransmission and its regulation by microRNAs (miR).

We also propose novel cellular and circuit mechanisms as contributing factors. Lastly, we discuss the implications of advancing our knowledge on SDL, both for most fundamental processes of learning and memory as well as for development and maintenance of psychopathology.”

Neurobiological correlates of state-dependent context fear

“Retrieval of fear memories can be state-dependent, meaning that they are best retrieved if the brain states at encoding and retrieval are similar. Such states can be induced by activating extrasynaptic γ-aminobutyric acid type A receptors (GABAAR) with the broad α-subunit activator gaboxadol. However, the circuit mechanisms and specific subunits underlying gaboxadol’s effects are not well understood.

Here we show that gaboxadol induces profound changes of local and network oscillatory activity, indicative of discoordinated hippocampal-cortical activity, that were accompanied by robust and long-lasting state-dependent conditioned fear. Episodic memories typically are hippocampus-dependent for a limited period after learning, but become cortex-dependent with the passage of time.

In contrast, state-dependent memories continued to rely on hippocampal GABAergic mechanisms for memory retrieval. Pharmacological approaches with α- subunit-specific agonists targeting the hippocampus implicated the prototypic extrasynaptic subunits (α4) as the mediator of state-dependent conditioned fear.

Together, our findings suggest that continued dependence on hippocampal rather than cortical mechanisms could be an important feature of state-dependent memories that contributes to their conditional retrieval.”


Here’s an independent 2017 Netherlands/UC San Diego review that should bring these researchers’ efforts to the VA’s attention:

MicroRNAs in Post-traumatic Stress Disorder

“Post-traumatic stress disorder (PTSD) is a psychiatric disorder that can develop following exposure to or witnessing of a (potentially) threatening event. A critical issue is to pinpoint the (neuro)biological mechanisms underlying the susceptibility to stress-related disorder such as PTSD, which develops in the minority of ~15% of individuals exposed to trauma.

Over the last few years, a first wave of epigenetic studies has been performed in an attempt to identify the molecular underpinnings of the long-lasting behavioral and mental effects of trauma exposure. The potential roles of non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) in moderating or mediating the impact of severe stress and trauma are increasingly gaining attention. To date, most studies focusing on the roles of miRNAs in PTSD have, however, been completed in animals, using cross-sectional study designs and focusing almost exclusively on subjects with susceptible phenotypes.

Therefore, there is a strong need for new research comprising translational and cross-species approaches that use longitudinal designs for studying trajectories of change contrasting susceptible and resilient subjects. The present review offers a comprehensive overview of available studies of miRNAs in PTSD and discusses the current challenges, pitfalls, and future perspectives of this field.”

Here’s a 2017 Netherlands human study that similarly merits the US Veterans Administration’s attention:

Circulating miRNA associated with posttraumatic stress disorder in a cohort of military combat veterans

“Posttraumatic stress disorder (PTSD) affects many returning combat veterans, but underlying biological mechanisms remain unclear. In order to compare circulating micro RNA (miRNA) of combat veterans with and without PTSD, peripheral blood from 24 subjects was collected following deployment, and isolated miRNA was sequenced.

PTSD was associated with 8 differentially expressed miRNA. Pathway analysis shows that PTSD is related to the axon guidance and Wnt signaling pathways, which work together to support neuronal development through regulation of growth cones. PTSD is associated with miRNAs that regulate biological functions including neuronal activities, suggesting that they play a role in PTSD symptomatology.”


See the below comments for reasons why I downgraded this review’s rating.

https://link.springer.com/article/10.1007/s11920-018-0887-x “Stress Response Modulation Underlying the Psychobiology of Resilience” (not freely available)

Faith-tainted epigenetics

This 2018 Loma Linda review subject was epigenetic interventions for aging:

“Epigenomic markers of aging, global DNA hypomethylation and promoter-specific hypermethylation may be engendered by iron and HCys [homocysteine] retention.

MiR-29/p53 axis may reverse age-related methylomic shifts, stabilizing both the genome and the epigenome, therefore removing a major risk factor of neurodegeneration. Lowering iron and HCys overload can be accomplished via chelation, blood donation and maintaining an adequate omega-6/omega-3 ratio.”


Sometimes it’s difficult to detect researchers’ biases. If a reader didn’t know about the funding sponsor’s mission:

“Each day we seek to extend the teaching and healing ministry of Jesus Christ”

they may view this paper as unbiased rather than as a directed narrative.

Consider the sponsor’s influence from the perspective of someone seeking treatment for Alzheimer’s disease. If a doctor in this review sponsor’s hospital system recommended chelation treatment, hope would be generated for the patient. Adopting the doctor’s belief about the treatment, though, would be contrary to other evidence per this review:

“In 2008, the NIH chelation trial stopped enrolling patients, approximately two years early.

There is no indication for exposing patients with dementia to the risks of chelation therapy because current chelators cannot help them.”

After reading another review that had this sponsor – The lack of oxygen’s epigenetic effects on a fetus – which also reflected the influence of the sponsor’s biases, and had a directed narrative that ignored evidence contradicting the narrative, and involved storytelling, I’m done curating any paper sponsored by this institution.

http://www.nrronline.org/downloadpdf.asp?issn=1673-5374;year=2018;volume=13;issue=4;spage=635;epage=636;aulast=Sfera;type=2 “Epigenetic interventions for brain rejuvenation: anchoring age-related transposons” (click the pdf button)

Manufacturing PTSD evidence with machine learning

What would you do if you were a scientist who had strong beliefs that weren’t borne out by experimental evidence?

Would you be honest with yourself about the roots of the beliefs? Would you attempt to discover why the beliefs were necessary for you, and what feelings were associated with the beliefs?

Instead of the above, the researchers of this 2017 New York human study reworked negative findings of two of the coauthors’ 2008 study until it fit their beliefs:

“The neuroendocrine response contributes to an accurate predictive signal of PTSD trajectory of response to trauma. Further, cortisol provides a stable predictive signal when measured in conjunction with other related neuroendocrine and clinical sources of information.

Further, this work provides a methodology that is relevant across psychiatry and other behavioral sciences that transcend the limitations of commonly utilized data analytic tools to match the complexity of the current state of theory in these fields.”


1. The limitations section included:

“It is important to note that ML [machine learning]-based network models are an inherently exploratory data analytic method, and as such might be seen as ‘hypotheses generating’. While such an approach is informative in situations where complex relationships cannot be proposed and tested a priori, such an approach also presents with inherent limitations as a high number of relationships are estimated simultaneously introducing a non-trivial probability of false discovery.”

2. Sex-specific impacts of childhood trauma summarized why cortisol isn’t a reliable biological measurement:

“Findings are dependent upon variance in extenuating factors, including but not limited to, different measurements of:

  • early adversity,
  • age of onset,
  • basal cortisol levels, as well as
  • trauma forms and subtypes, and
  • presence and severity of psychopathology symptomology.”

Although this study’s authors knew or should have known that review’s information, cortisol was the study’s foundation, and beliefs in its use as a biomarker were defended.

3. What will it take for childhood trauma research to change paradigms? described why self-reports of childhood trauma can NEVER provide direct evidence for trauma during the top three periods when humans are most sensitive to and affected by trauma:

The basic problem prohibiting the CTQ (Childhood Trauma Questionnaire) from discovering likely most of the subjects’ historical traumatic experiences that caused epigenetic changes is that these experiences predated the CTQ’s developmental starting point.

Self-reports were – at best – evidence of experiences after age three, distinct from the experience-dependent epigenetic changes since conception.”

Yet the researchers’ beliefs in the Trauma History Questionnaire’s capability to provide evidence for early childhood traumatic experiences allowed them to make such self-reports an important part of this study’s findings, for example:

“The reduced cortisol response in the ER [emergency room] was dependent on report of early childhood trauma exposure.”

https://www.nature.com/articles/tp201738 “Utilization of machine learning for prediction of post-traumatic stress: a re-examination of cortisol in the prediction and pathways to non-remitting PTSD”