The arrogance of a paradigm exceeding its evidence

This 2018 commentary from the American College of Emergency Physicians by 7 physicians discussed the harm that will result from imposing a mandatory paradigm of sepsis treatment. I’ll quote sections that mention evidence:

“These metrics [for pneumonia treatment] had little evidentiary basis but led to an institutional-fostered culture of overdiagnosis and overtreatment. Have we learned from this folly or does a new sepsis guideline promote similar time-based treatment strategies with little direct supporting evidence?

Like the pneumonia quality measure, this resource-heavy care flows from an overreaching interpretation of evidence. Despite that evidence consistently fails to find a benefit of a single treatment strategy, the Surviving Sepsis Campaign continues to promote recommendations that bypass the individual clinician’s judgment.

Although well intentioned, the current sepsis bundles and the potential penalties associated with noncompliance lay a heavy weight on ED [emergency department] care absent evidence that a net benefit will follow. The proposed Surviving Sepsis Campaign abbreviated bundle heightens the burden by further restricting the time allotted for the identification and treatment of patients with suspected sepsis, all without any evidence of benefit or knowledge of the logistic consequences or cost.”


The paradigm’s promoters didn’t learn the appropriate lessons from “the sense of embarrassment and regret once experienced with the pneumonia quality metric.”

What do you think are the root causes of the Surviving Sepsis Campaign’s agenda?

  • Did it start with lawyers? Lawsuits can force hospitals into actions for which the primary reason is to avoid “the potential penalties associated with noncompliance.”
  • Is it due to governments? Governments can force hospitals into actions “without any evidence of benefit or knowledge of the logistic consequences or cost” when the hospitals accept government reimbursement.
  • Did it start with other groups of unaccountable people who think they know better than everyone else about how others should act?

https://www.sciencedirect.com/science/article/pii/S0196064418306073 “The 2018 Surviving Sepsis Campaign’s Treatment Bundle: When Guidelines Outpace the Evidence Supporting Their Use” (not freely available)

Advertisements

Epigenetic transgenerational inheritance of ovarian disease

This 2018 Washington rodent study investigated ovarian disease in F3 great-granddaughters caused by their F0 great-grandmothers’ exposures to DDT or vinclozolin while pregnant:

“Two of the most prevalent ovarian diseases affecting women’s fertility and health are Primary Ovarian Insufficiency (POI) and Polycystic Ovarian Syndrome (PCOS). POI is characterized by a marked reduction in the primordial follicle pool of oocytes and the induction of menopause prior to age 40. POI currently affects approximately 1% of female population. While genetic causes can be ascribed to a minority of patients, around 90% of POI cases are considered idiopathic, with no apparent genetic link nor known cause.

PCOS is a multi-faceted disease that affects 6-18% of women. It is characterized by infrequent ovulation or anovulation, high androgen levels in the blood, and the presence of multiple persistent ovarian cysts.

For both PCOS and POI other underlying causes such as epigenetic transgenerational inheritance of disease susceptibility have seldom been considered. Epigenetic transgenerational inheritance is defined as “the germline transmission of epigenetic information and phenotypic change across generations in the absence of any continued direct environmental exposure or genetic manipulation.” Epigenetic factors include:

  • DNA methylation,
  • Histone modifications,
  • Expression of noncoding RNA,
  • RNA methylation, and
  • Alterations in chromatin structure.

The majority of transgenerational studies have examined sperm transmission of epigenetic changes due to limitations in oocyte numbers for efficient analysis.

There was no increase in ovarian disease in direct fetal exposed F1 [grandmothers] or germline exposed F2 [mothers] generation vinclozolin or DDT lineage rats compared to controls.

The transgenerational molecular mechanism is distinct and involves the germline (sperm or egg) having an altered epigenome that following fertilization may modify the embryonic stem cells epigenome and transcriptome. This subsequently impacts the epigenetics and transcriptome of all somatic cell types derived from these stem cells.

Therefore, all somatic cells in the transgenerational [F3] animal have altered epigenomes and transcriptomes and those sensitive to this alteration will be susceptible to develop disease. The F3 generation can have disease while the F1 and F2 generations do not, due to this difference in the molecular mechanisms involved.

The epimutations and gene expression differences observed are present in granulosa cells in the late pubertal female rats at 22-24 days of age, which is long before any visible signs of ovarian disease are detectable. This indicates that the underlying factors that can contribute to adult-onset diseases like PCOS and POI appear to be present early in life.

Ancestral exposure to toxicants is a risk factor that must be considered in the molecular etiology of ovarian disease.”


1. The study highlighted a great opportunity for researchers of any disease that frequently has an “idiopathic” diagnosis. It said a lot about research priorities that “around 90% of POI cases are considered idiopathic, with no apparent genetic link nor known cause.”

It isn’t sufficiently explanatory for physicians to continue using categorization terminology from thousands of years ago. Science has progressed enough with measured evidence to discard the “idiopathic” category and express probabilistic understanding of causes.

2. One of this study’s coauthors made a point worth repeating in The imperative of human transgenerational studies: What’s keeping researchers from making a significant difference in their fields with human epigenetic transgenerational inheritance studies?

3. Parts of the study’s Discussion section weren’t supported by its evidence. The study didn’t demonstrate:

  • That “all somatic cells in the transgenerational animal have altered epigenomes and transcriptomes”; and
  • The particular “molecular mechanisms involved” that exactly explain why “the F3 generation can have disease while the F1 and F2 generations do not.”

https://www.tandfonline.com/doi/abs/10.1080/15592294.2018.1521223 “Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Ovarian Pathology and Granulosa Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Polycystic Ovarian Syndrome and Primary Ovarian Insuf[f]iency” (not freely available)

Reversing epigenetic changes with CRISPR/Cas9

This 2018 Chinese review highlighted areas in which CRISPR/Cas9 technology has, is, and could be applied to rewrite epigenetic changes:

“CRISPR/Cas9-mediated epigenome editing holds a great promise for epigenetic studies and therapeutics.

It could be used to selectively modify epigenetic marks at a given locus to explore mechanisms of how targeted epigenetic alterations would affect transcription regulation and cause subsequent phenotype changes. For example, inducing histone methylation or acetylation at the Fosb locus in the mice brain reward region, nucleus accumbens, could affect relevant transcription network and thus control behavioral responses evoked by drug and stress.

Epigenome editing has the potential for epigenetic treatment, especially for the disorders with abnormal gene imprinting or epigenetic marks. Targeted epigenetic silencing or reactivation of the mutant allele could be a potential therapeutic approach for diseases such as Rett syndrome and Huntington’s disease.

Noncoding RNA plays important roles in gene imprinting and chromatin remodeling. CRISPR/Cas9 has been shown to be potential for manipulating noncoding RNA expression, including microRNA, long noncoding RNA, and miRNA families and clusters.

In vivo overexpression of the Yamanaka factors have proven to be able to fully or partially help somatic cells to regain pluripotency in situ. These rejuvenated cells would subsequently differentiate again to replace the lost cell types.”


The last paragraph was described in The epigenetic clock theory of aging as a promising technique:

“To date, the most effective in vitro intervention against epigenetic ageing is achieved through expression of Yamanaka factors, which convert somatic cells into pluripotent stem cells, thereby completely resetting the epigenetic clock.”

The reviewers cited three references for in vivo studies of this technique. Overall, I didn’t see that any of the review’s references were in vivo human studies.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6079388/ “Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System”

Epigenetic factors affecting female rat sexual behavior

This 2018 Baltimore/Montreal rodent study found:

“If sexually naïve females have their formative sexually rewarding experiences paired with the same male, they will recognize that male and display mate-guarding behavior towards him in the presence of a female competitor. Female rats that display mate-guarding behavior also show enhanced activation of oxytocin and vasopressin neurons in the supraoptic and paraventricular hypothalamic nucleus.

We examined the effect of a lysine-specific demethylase-1 inhibitor to block the action of demethylase enzymes and maintain the methylation state of corresponding genes. Female rats treated with the demethylase inhibitor failed to show any measure of mate guarding, whereas females treated with vehicle displayed mate guarding behavior. Demethylase inhibitor treatment also blocked the ability of familiar male cues to activate oxytocin and vasopressin neurons, whereas vehicle-treated females showed this enhanced activation.”

General principles and their study-specific illustrations were:

Histone modifications are a key element in gene regulation through chromatin remodeling. Histone methylation / demethylation does not have straightforward transcriptional outcomes as do other histone modifications, like acetylation, which is almost invariably associated with transcriptional activation.

What is of vital importance in regards to histone methylation / demethylation is the pattern of methylation that is established. Patterns of methylation incorporate both methylated and demethylated residues, and are what ultimately play a role in transcriptional outcomes.

In the present study, inhibiting LSD1 demethylase enzymes disrupted the ability of cells to properly establish histone methylation / demethylation patterns, thus creating a deficit in the cells’ ability to transcribe the gene products necessary for the enhanced induction of OT, AVP, and the subsequent mate-guarding behaviors we observed. This study is the first to demonstrate a definitive role of epigenetic histone modifications in a conditioned sexual response.”

https://www.sciencedirect.com/science/article/pii/S0031938418303421 “Inhibition of lysine-specific demethylase enzyme disrupts sexually conditioned mate guarding in the female rat” (not freely available)

Hijacking the epigenetic clock paradigm

This 2018 German human study’s last sentence was:

“Additionally we found an association between DNAm [DNA methylation] age acceleration and rLTL [relative leukocyte telomere length], suggesting that this epigenetic clock, at least partially and possibly better than other epigenetic clocks, reflects biological age.”

Statements in the study that contradicted, qualified, and limited the concluding sentence included:

“The epigenetic clock seems to be mostly independent from the mitotic clock as measured by the rLTL.

It could be possible that associations are confounded due to short age ranges or non-continuous age distribution, as displayed in the BASE-II cohort (no participants between the age of 38 and 59 years). [see the below graphic]

The BASE-II is a convenience sample and participants have been shown to be positively selected with respect to education, health and cognition.

Samples in which DNAm age and chronological age differed more than three standard deviations from the mean were excluded (N=19).

While the original publication employed eight CpG sites for DNAm age estimation, we found that one of these sites did not significantly improve chronological age prediction in BASE-II. Thus, we reduced the number of sites considered to seven in the present study and adapted the algorithm to calculate DNAm age.

  • Horvath described a subset of 353 methylation sites predicting an individual’s chronological age with high accuracy..
  • Even though the available methods using more CpG sites to estimate DNAm age predict chronological age with higher accuracy..
  • It is not clear how much of the deviation between chronological age and DNAm age reflects measurement error/low number of methylation sites and which proportion can be attributed to biological age.

Due to the statistical method employed, we encountered a systematic deviation of DNAm age in our dataset.”


Findings that aren’t warranted by the data is an all-too-common problem with published research. This study illustrated how researcher hypothesis-seeking behavior – that disregarded what they knew or should have known – can combine with a statistics package to produce almost any finding.

It reminded me of A skin study that could have benefited from preregistration that made a similar methodological blunder:

The barbell shape of the subjects’ age distribution wouldn’t make sense if the researchers knew they were going to later use the epigenetic clock method.

The researchers did so, although the method’s instructive study noted:

“The standard deviation of age has a strong relationship with age correlation”

and provided further details in “The age correlation in a data set is determined by the standard deviation of age” section.

Didn’t the researchers, their organizations, and their sponsors realize that this study’s problematic design and performance could misdirect readers away from the valid epigenetic clock evidence they referenced? What purposes did it serve for them to publish this study?

https://academic.oup.com/biomedgerontology/advance-article-abstract/doi/10.1093/gerona/gly184/5076188 “Epigenetic clock and relative telomere length represent largely different aspects of aging in the Berlin Aging Study II (BASE-II)” (not freely available)

The role of recall neurons in traumatic memories

This 2018 Swiss rodent study found:

“Our data show that:

  • A subset of memory recall–induced neurons in the DG [dentate gyrus] becomes reactivated after memory attenuation,
  • The degree of fear reduction positively correlates with this reactivation, and
  • The continued activity of memory recall–induced neurons is critical for remote fear memory attenuation.

Although other brain areas such as the prefrontal cortex and the amygdala are likely to be implicated in remote fear memories and remain to be investigated, these results suggest that fear attenuation at least partially occurs in memory recall–induced ensembles through updating or unlearning of the original memory trace of fear.

These data thereby provide the first evidence at an engram-specific level that fear attenuation may not be driven only by extinction learning, that is, by an inhibitory memory trace different from the original fear trace.

Rather, our findings indicate that during remote fear memory attenuation both mechanisms likely coexist, albeit with the importance of the continued activity of memory recall–induced neurons experimentally documented herein. Such activity may not only represent the capacity for a valence change in DG engram cells but also be a prerequisite for memory reconsolidation, namely, an opportunity for learning inside the original memory trace.

As such, this activity likely constitutes a physiological correlate sine qua non for effective exposure therapies against traumatic memories in humans: the engagement, rather than the suppression, of the original trauma.”

The researchers also provided examples of human trauma:

“We dedicate this work to O.K.’s father, Mohamed Salah El-Dien, and J.G.’s mother, Wilma, who both sadly passed away during its completion.”


So, how can this study help humans? The study had disclosed and undisclosed limitations:

1. Humans aren’t lab rats. We can ourselves individually change our responses to experiential causes of ongoing adverse effects. Standard methodologies can only apply external treatments.

2. It’s a bridge too far to go from neural activity in transgenic mice to expressing unfounded opinions on:

“A physiological correlate sine qua non for effective exposure therapies against traumatic memories in humans.”

Human exposure therapies have many drawbacks, in addition to being applied externally to the patient on someone else’s schedule. A few others were discussed in The role of DNMT3a in fear memories:

  • “Inability to generalize its efficacy over time,
  • Potential return of adverse memory in the new/novel contexts,
  • Context-dependent nature of extinction which is widely viewed as the biological basis of exposure therapy.”

3. Rodent neural activity also doesn’t elevate recall to become an important goal of effective human therapies. Clearly, what the rodents experienced should be translated into human reliving/re-experiencing, not recall. Terminology used in animal studies preferentially has the same meaning with humans, since the purpose of animal studies is to help humans.

4. The researchers acknowledged that:

“Other brain areas such as the prefrontal cortex and the amygdala are likely to be implicated in remote fear memories and remain to be investigated.”

A study that provided evidence for basic principles of Primal Therapy determined another brain area:

“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.”

The study I curated yesterday, Organ epigenetic memory, demonstrated organ memory storage. It’s hard to completely rule out that other body areas may also store traumatic memories.

The wide range of epigenetic memory storage vehicles is one reason why effective human therapies need to address the whole person, the whole body, and each individual’s entire history.

http://science.sciencemag.org/content/360/6394/1239 “Reactivation of recall-induced neurons contributes to remote fear memory attenuation” (not freely available)

Here’s one of the researchers’ outline:


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.

Organ epigenetic memory

This 2018 Japanese review subject was the relationships of organ memory and non-communicable diseases:

“Organ memory is the engraved phenotype of altered organ responsiveness acquired by a time-dependent accumulation of organ stress responses. This phenomenon is known as “metabolic memory” or “legacy effect,” which is similar to neuronal and immune memory.

Not only is the epigenetic change of key genes involved in the formation of organ memory but the alteration of multiple factors, including low molecular weight energy metabolites, immune mediators, and tissue structures, is involved as well. These factors intercommunicate during every stress response and carry out incessant remodeling in a certain direction in a spiral fashion through positive feedback mechanisms.

The systematic review revealed that each intervention type, that is:

  • Glucose lowering,
  • Blood pressure lowering, or
  • LDL-cholesterol lowering,

possessed unique characteristics of the memory phenomenon. Most of the observational periods of these studies lasted for > 10 years. Memory phenomenon was suggested to last for a long time and is thought to have a considerable effect on the clinical course of NCDs [non-communicable diseases].

Organs cannot possess consciousness, so it might not be appropriate to consider whether a recalling process exists in organs. However, the properties of organs are incessantly altered by external stimuli loaded on organs as if it is updating.

It is clinically important to investigate whether organ memory can be updated by our behaviors. Once organ memory is established in an organ, organ memory in each organ can influence one another and affect organ memory in a different organ.

Epigenome-modification enzymes, such as histone deacetylases and DNA methyltransferases, and transcription factors seem to be essential for the epigenetic regulation of gene expression, which is involved in the generation of organ memory. Cellular metabolism can epigenetically modulate the expression of genes that are related to the progression of diseases.”


The reviewers asserted:

“Organs cannot possess consciousness, so it might not be appropriate to consider whether a recalling process exists in organs.”

Memory studies don’t require this consciousness to investigate even the brain organ’s areas and functions. Researchers observe memory by measuring stimulus/response items like neuron activation and various levels of behavior. Consciousness is an emergent property.

Regarding recall: An organ’s “engraved phenotype of altered organ responsiveness” may not have recall itself, but it doesn’t have a separate existence apart from its body. An organ can’t be removed from its body for very long and still be part of its body.

When an organ is in its normal state as part of a body, it has access to recall-like functions via the “inter-organ communication of organ memory.” The review also mentioned:

“Organ memory in each organ can influence one another and affect organ memory in a different organ.

Evolution didn’t support unnecessary duplication for a kidney’s memory to include recall because it’s part of a body that includes a brain that has recall. Evolution didn’t duplicate functions of a kidney’s memory in a brain, either.

https://www.nature.com/articles/s41440-018-0081-x “Organ memory: a key principle for understanding the pathophysiology of hypertension and other non-communicable diseases” (not freely available)