Evaluating a company-sponsored β-glucan paper

This 2020 review subject was yeast cell wall β-glucan effects in humans:

“The first aim of this review is to collate and interpret the existing pre‐clinical research on β‐1,3/1,6‐glucan with regard to immunity in order to clarify its molecular mechanism of immunomodulatory action.


The second aim of this review is to collate and evaluate the literature in order to provide a comprehensive overview of human studies assessing the effect of supplementation with high quality, well‐characterized β‐1,3/1,6‐glucan from commercially available sources on immunity across multiple populations. Inclusion criteria consist of randomized, double‐blind, placebo‐controlled human studies that investigated efficacy of orally administered β‐glucan with a purity of over 75%.”

https://onlinelibrary.wiley.com/doi/10.1002/mnfr.201901071 “β‐1,3/1,6‐Glucans and Immunity: State of the Art and Future Directions”

I don’t usually curate company-sponsored research, aka puff pieces. I wondered why, after taking WellImmune β-glucan 500 mg daily for over two months, I didn’t have expected results.

There are always several possible explanations for experimental failures. I didn’t see applicable items in this paper.

There was much information regarding things their sponsor’s customers don’t need to know. Just like their sponsor’s product label, there was little about what customers need to know, such as:

What was each product’s content, in specific percentages, of 1,3/1,6 terminal-linked glucose molecules? That makes a difference.

The sponsor knows, but doesn’t disclose it on their product’s label. These researchers could have found out and presented that information on their sponsor’s and other companies’ products for each study reviewed.

Not doing so deprived readers of an important evaluation criteria that could possibly explain variable results and provide a better measure for comparability. Stopping at “a purity of over 75%” instead of investigating and disclosing exact information was evasive.

A broccoli sprouts study that lacked evidence for human applicability

A 2020 study Combined Broccoli Sprouts and Green Tea Polyphenols Contribute to the Prevention of Estrogen Receptor–Negative Mammary Cancer via Cell Cycle Arrest and Inducing Apoptosis in HER2/neu Mice (not freely available) conclusion was:

“Lifelong BSp [broccoli sprouts] and GTP [green tea polyphenol] administration can prevent estrogen receptor–negative mammary tumorigenesis through cell cycle arrest and inducing apoptosis in HER2/neu mice.”

These researchers had unaddressed insufficiencies in this study that were also in their 2018 study as curated below. The largest item that required translation into human applicability was rodent diet content of 26% “broccoli sprout seeds.”

You may be surprised to read the below previous study’s unevidenced advice to eat double the weight of broccoli sprouts that I eat every day. You won’t be surprised that it’s not going to happen. Especially when no alternatives were presented because rodent diet details weren’t analyzed and published.

Sulforaphane is an evolved defense mechanism to ward off predators, and eating it is evolutionarily unpleasant. Will people in general and pregnant women in particular eat a diet equivalent to 26% “broccoli sprout seeds?”

Where were peer reviewer comments and researcher responses? Are these not public as they are by all Open Access journals hosted on https://www.mdpi.com/?

Sponsors and researchers become locked into paradigms that permit human-inapplicable animal research year after year. What keeps them from developing sufficient human-applicable evidence to support their hypotheses?

This 2018 Alabama rodent study investigated the epigenetic effects on developing breast cancer of timing a sulforaphane-based broccoli sprouts diet. Timing of the diet was as follows:

  1. Conception through weaning (postnatal day 28), named the Prenatal/maternal BSp (broccoli sprouts) treatment (what the mothers ate starting when they were adults at 12 weeks until their pups were weaned; the pups were never on a broccoli sprouts diet);
  2. Postnatal day 28 through the termination of the experiment, named the Postnatal early-life BSp treatment (what the offspring ate starting at 4 weeks; the mothers were never on a broccoli sprouts diet); and
  3. Postnatal day 56 through the termination of the experiment, named the Postnatal adult BSp treatment (what the offspring ate starting when they were adults at 8 weeks; the mothers were never on a broccoli sprouts diet).

“The experiment was terminated when the mean tumor diameter in the control mice exceeded 1.0 cm.

Our study indicates a prenatal/maternal BSp dietary treatment exhibited maximal preventive effects in inhibiting breast cancer development compared to postnatal early-life and adult BSp treatments in two transgenic mouse models that can develop breast cancer.

Postnatal early-life BSp treatment starting prior to puberty onset showed protective effects in prevention of breast cancer but was not as effective as the prenatal/maternal BSp treatment. However, adulthood-administered BSp diet did not reduce mammary tumorigenesis.

The prenatal/maternal BSp diet may:

  • Primarily influence histone modification processes rather than DNA methylation processes that may contribute to its early breast cancer prevention effects;
  • Exert its transplacental breast cancer chemoprevention effects through enhanced histone acetylation activator markers due to reduced HDAC1 expression and enzymatic activity.

This may be also due to the importance of a dietary intervention window that occurs during a critical oncogenic transition period, which is in early life for these two tested transgenic mouse models. Determination of a critical oncogenic transition period could be complicated in humans, which may partially explain the controversial findings of the adult BSp treatment on breast cancer development in the tested mouse models as compared the previous studies. Thus long-term consumption of BSp diet is recommended to prevent cancers in humans.”

“The dietary concentration for BSp used in the mouse studies was 26% BSp in formulated diet, which is equivalent to 266 g (~4 cups) BSp/per day for human consumption. The concentration of BSp in this diet is physiological available and represents a practical consumption level in the human diet.

Prior to the experiment, we tested the potential influences of this prenatal/maternal BSp regimen on maternal and offspring health as well as mammary gland development in the offspring. Our results showed there was no negative effect of this dietary regimen on the above mentioned factors (data not shown) suggesting this diet is safe to use during pregnancy.”

I didn’t see where the above-labelled “Broccoli Sprout Seeds” diet content was defined. It’s one thing to state:

“SFN as the most abundant and bioactive compound in the BSp diet has been identified as a potent HDAC inhibitor that preferably influences histone acetylation processes.”

and describe how sulforaphane may do this and may do that, and include it in the study’s title. It’s another thing to quantify an animal study into findings that can help humans.

The study’s food manufacturer offers dietary products to the public without quantifying all contents. Good for them if they can stay in business by serving customers who can’t be bothered with scientific evidence.

Any difference between the above-labelled “Broccoli Sprout Seeds” and broccoli seeds? Where was any evidence that “Broccoli Sprout Seeds” and SPROUTED “Broccoli Sprout Seeds” were equivalent per this claim:

“Equivalent to 266 g (~4 cups) BSp/per day for human consumption. The concentration of BSp in this diet is physiological available and represents a practical consumption level in the human diet.”

To help humans, this animal study had to have more details than the food manufacturer provided. These researchers should have either tasked the manufacturer to specify “Broccoli Sprout Seeds” content, or contracted out analysis if they weren’t going to do it themselves.

Regarding timing of a broccoli sprouts diet for humans, this study didn’t provide evidence for recommending:

“Long-term consumption of BSp diet is recommended to prevent cancers in humans.”

http://cancerpreventionresearch.aacrjournals.org/content/early/2018/05/15/1940-6207.CAPR-17-0423.full-text.pdf “Temporal efficacy of a sulforaphane-based broccoli sprout diet in prevention of breast cancer through modulation of epigenetic mechanisms”

Measuring one dimension of health

This 2020 human study asserted:

“Our data provides the first epidemiological evidence supporting evidence obtained in preclinical models of metabolic syndrome and NAFLD that demonstrated hepatoprotective effects of phenolic acids.

  • High dietary intake of total phenolic acids is associated with a lower prevalence of non-alcoholic fatty liver disease and insulin resistance.
  • High intake of hydroxybenzoic acids, a class of phenolic acids, is associated with a lower prevalence of steatosis and clinically significant fibrosis.
  • High intake of hydroxycinnamic acids, another class of phenolic acids, is associated with a lower prevalence of insulin resistance.

Data on polyphenol content in foods was obtained from the Phenol-Explorer database (www.phenol-explorer.eu).”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078532/ “Higher phenolic acid intake independently associates with lower prevalence of insulin resistance and non-alcoholic fatty liver disease”

It’s a bad weather day, so I investigated the phenolics database and ran some numbers:

coffee and tea phenolics

Phenolic contents of all the other food I eat is 9% of my coffee-and-tea 1,975 mg total phenolics. Microwaved broccoli sprouts contribute half of that 9%.

Subjects were grouped according to whether their phenolics daily intake was over 221 mg or not. The over 221 mg group drank 5 cups of coffee a day, whereas the other group drank 1 cup.

According to a phenolics dimension of health, all these researchers needed to do was ask subjects about their daily coffee intake. But then the study would be over, with few “is associated with” findings.

Do humans avoid insulin resistance and non-alcoholic fatty liver disease by drinking more than one cup of coffee and tea? Is an answer available from real people, not just from a statistics package?

A 2020 study that primarily sourced a database last updated in June 2015 selected a fertile ground for later hypothesis-seeking.

fitting data

Ignoring subsequent research helped when staking a claim of first for whatever niche provided a publication opportunity.

I didn’t upload a screenshot of the Excel workbook with entries for pictured items I eat every day. That June 2015 database was incomplete with respect to current science here in December 2020.

See Eat oats today! for current examples of phenolic compounds in my daily 81 grams of steel-cut oats.

Does reprogramming signaling pathways create memories?

This 2020 study investigated genes and signaling pathways for inflammatory memory:

“Fibroblast-like synoviocytes (FLS) play a critical role in pathogenesis of rheumatoid arthritis (RA). Chronic inflammation induces transcriptomic and epigenetic modifications that imparts a persistent catabolic phenotype to the FLS, despite their dissociation from the inflammatory environment.

Sustained activated genes established pro-inflammatory signaling components known to act at multiple levels of NF-κB, STAT and AP-1 signaling cascades. Sustained repressed genes included critical mediators and targets of the BMP [bone morphogenic protein] signaling pathway.

We identified sustained repression of BMP signaling as a unique constituent of the long-term inflammatory memory induced by chronic inflammation.

FLS are synovial tissue-resident and specialized mesenchymal cells critical for homeostasis. Key features of these cells during homeostasis include the production of extracellular matrix components and providing nutrients to the synovial fluid. Healthy synovium is composed of multiple layers of FLS, which forms the synovial lining and sublining through cell–cell contacts.

Inflammatory and pro-resolving mediators are tightly regulated to maintain normal synovium functioning. However, in inflammatory and autoimmune diseases such as rheumatoid arthritis, an imbalance between these signals causes homeostasis disruption leading to synovial tissue damage, cartilage destruction and bone degeneration.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679373/ “Chronic exposure to TNF reprograms cell signaling pathways in fibroblast-like synoviocytes by establishing long-term inflammatory memory”

These researchers described a positive feedback loop that kept rheumatoid arthritis in place. No feedback diagram or explanation of what sustained a disease condition other than to say:

“Gene expression changes induced by short-term tumor necrosis factor-alpha (TNF-α) treatment were largely sustained in the FLS exposed to chronic inflammation.”

Okay – then what upstream signals sustained TNF-α? What would it take to interrupt that feedback loop? What initiated it?

Studies usually substantiate effects by also developing evidence for causes of opposite effects and of no effects. This study investigated neither reversibility nor no effect, and instead stated:

“Multiple signaling networks are irreversibly modified due to TNF-α-mediated long-term epigenetic and transcriptomic reprogramming. We speculate that sustained repression of BMP signaling may be critically required to ensure the persistently transformed phenotype of RA FLS.”

No evidence was offered for “irreversibly modified.” Anyway, that didn’t fit with:

“We postulate that simultaneous targeting of these activated and repressed signaling pathways may be necessary to combat RA persistence.”

Enduring epigenetic memories? Or continuous toxic stimulation? provided another perspective: “Enduring epigenetic effects may be symptoms rather than causes when toxic conditions persist.”

Been on a Steely Dan kick lately. Probably due to this year’s Royal Scam:

A cherry-picked DNA methylation study

This 2020 US/Sweden/Denmark human study measured twins during their old age:

“We evaluate individual differences in DNA methylation at individual CpG sites across the methylome across 10 years in two Scandinavian samples of same‐sex aging twins. We test two competing hypotheses about the longitudinal stability and change in DNA methylation:

  1. The contribution of genetic influences changes with age, reflecting diminishing influence across time; and
  2. Nonshared factors accumulate in importance, signaling an increasing diversity of response to environmental exposures.

Understanding epigenetic changes over time in the elderly may identify pathways of decline or plasticity (e.g., maintenance or even boosts in functioning) during the aging process and help with elucidating the biology of aging and survival.

Across time, stability in methylation is primarily due to genetic contributions, while novel experiences and exposures contribute to methylation differences. Elevated genetic contributions at age‐related methylation sites suggest that adaptions to aging and senescence may be differentially impacted by genetic background.”

https://onlinelibrary.wiley.com/doi/full/10.1111/acel.13197 “A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation”

Swedish subject measurements were taken at ages 62 and 72. Danish subject measurements were taken at ages 76 and 86.

One epigenetic clock that used 2019 technology was favored over three others, including Horvath’s 2013 original clock. For some reason this study didn’t use his 2018 skin-and-blood clock that had vastly improved technology such as an 18-fold increase in genomic coverage with Illumina 450k/850k bead arrays.

These researchers’ intentions became evident with:

“The 353 Horvath clock sites were selected as best predictors of chronological age using multiple tissues. The 71 Hannum clock sites best predicted age (adjusted for sex, BMI) based on methylation observed in whole blood while the 514 sites from the Zhang prediction model relied on methylation observed in blood and saliva samples (Zhang et al., 2019).

The current findings of moderately higher heritabilities in the Zhang and Hannum sites versus the other clock sites may be in part due to our use of blood tissue.”

The 18-fold increase improved accuracy in blood for the 2018 Horvath clock. Could these researchers ignore it and claim they did their due diligence in 2019 and 2020?

A larger issue was this study’s duality paradigm of either heritability or environment being solely responsible for observed changes. Consider what A blood plasma aging clock found at ages 60 and 78 peaks:

The above changes were due to life stage. Josh Mitteldorf did his usual excellent job of providing contexts for that study with New Aging Clock based on Proteins in the Blood, including:

“The implication is that a more accurate clock can be constructed if it incorporates different information at different life stages. None of the Horvath clocks have been derived based on different CpG sites at different ages, and this suggests an opportunity for a potential improvement in accuracy.”

Weren’t changes in subjects’ life stages relevant to their epigenetic changes? Why wouldn’t their life stages have been among the causes of observed effects?

Measuring sulforaphane plasma compounds

This 2020 Australian human study investigated methods of measuring sulforaphane plasma compounds:

“A simplified methodology to allow high-throughput LC–MS [Liquid Chromatography-Mass Spectrometry] analysis of plasma samples for measurement of sulforaphane and its metabolites is described. Analysis time is greatly reduced by employing fast chromatography and simple plasma extraction procedure.

Participants were observed consuming four Broccomax capsules, each containing 30 mg of broccoli seed extract and a dose of 8 mg of sulforaphane, as per manufacturer certificate of analysis, resulting in a total dose of 32 mg of sulforaphane (120 mg of broccoli seed extract).

Mean peak of combined metabolites from our study (0.9 and 1 μM) using 120 mg of broccoli seed extract (~32 mg of SFN) was similar to work by Fahey et al. who investigated pharmacokinetics of 350 mg of purified broccoli seed powder (mean 1.3 μM ± 0.5 μM), though our dose was almost three-times less. Pharmacokinetic profiles of our study mirrored those of Fahey et al. in that excretion was complete 8 hrs after consumption. Our intervention peaked slightly later (~2hrs), than that of Fahey (~1 hr), likely due to our use of a capsule rather than liquid.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070302/ “Measuring Sulforaphane and Its Metabolites in Human Plasma: A High Throughput Method”

This study was thin on comparing their n=2 results to previous work. Here are comparables from Broccoli or Sulforaphane: Is It the Source or Dose That Matters?

These researchers set up a strawman by stating a false comparison:

“Our dose was almost three-times less.”

The compared study was the n = 10 subjects row above, which stated its dose as:

“200 μmol of SF was contained in about 350 mg of SF-αCD powder dissolved in 25 mL of distilled water, which subjects were given to drink upon arrival at the clinic.”

If the current study wanted a true comparison, they would measure and compare sulforaphane dose weights or amounts:

  • https://pubchem.ncbi.nlm.nih.gov/compound/sulforaphane lists sulforaphane’s molecular weight as 177.3 g / mol.
  • A 5.64 μmol sulforaphane amount (.001 / 177.3) equals a 1 mg weight of sulforaphane.
  • 200 μmol / 5.64 μmol = 35 mg sulforaphane used in the compared study.

But these researchers couldn’t even do that! They asserted a 32 mg sulforaphane dose “per manufacturer certificate of analysis” when they had the resources to do otherwise!

What kind of study design would go to all the trouble of measuring plasma sulforaphane metabolite outputs, but not measure their sulforaphane input dose???

Had they closely read the compared study, they may have also noticed that its commercial supplement, Prostaphane, was tested to verify stated dosage. These researchers could have done the same with Broccomax.

Don’t overcook broccoli

This 2020 US / Korea study set a low bar and jumped over it by finding:

“The abundance of GSL [glucosinolate] hydrolysis products in cooked samples was lower compared to the raw samples.

Regardless of different cooking methods and durations, the total GSL amount in MeJA [methyl jasmonate]-treated broccoli was still higher than in the non-treated broccoli. This suggests that the increased GSL concentration in broccoli samples was solely affected by MeJA treatment, and the effect of MeJA was not affected by cooking methods.

Effect of cooking and 250 µM MeJA treatment on (A) total aliphatic glucosinolates, (B) total indole glucosinolates, and (C) total glucosinolates in ‘Green Magic’ broccoli. * = detected significant different by Student’s T-test (p ≤ 0.05, n = 3) with a significant interaction between MeJA treatment and cooking treatment.”

https://www.mdpi.com/2304-8158/9/6/758/htm “Methyl Jasmonate Treatment of Broccoli Enhanced Glucosinolate Concentration, Which Was Retained after Boiling, Steaming, or Microwaving”

Did it advance science to only replicate mistakes in consumer broccoli cooking methods with:

“The abundance of GSL hydrolysis products in cooked samples was lower compared to the raw samples.”


Did the study design have tests to provide cooking method guidance for:

“To date, methods of delivering cooked broccoli without losing its nutritional benefits are still lacking in the literature, although consuming cooked broccoli is the most common practice for consumers.”


Were there cooking method and temperature recommendations to avoid:

“Cooking also inactivates myrosinase, the enzyme converting GSL into hydrolysis products, and then hinders the formation of hydrolysis products.”


Were there cooking method tests to further enhance either control samples or:

“Exogenous methyl jasmonate (MeJA) treatment was known to increase the levels of neoglucobrassicin and their bioactive hydrolysis products in broccoli.”


Why omit temperature measurements since:

“The major research questions of this study were to evaluate how MeJA application to broccoli plants will affect GSL concentration, myrosinase activity, GSL hydrolysis product amounts..”

Maybe Microwave broccoli to increase sulforaphane levels wasn’t yet published when this study’s design decisions were made. Still, why would a study:

  • Test microwave half power without also testing full power?
  • Select microwaving time as the sole measurement without also measuring temperature?

Table S1 and Figure 3 of the Chinese / USDA study showed a two-minute microwaving time at 50% power wouldn’t be expected to have any sulforaphane content significantly different from uncooked broccoli. Also, temperatures of a five-minute microwaving time at 50% power were guaranteed to completely deactivate myrosinase.

Supplementary material confirmed that this study’s microwaving parameters didn’t show anything of value for how to use your microwave to increase broccoli compound levels. Did the study’s findings provide much more than what not to do?

Poor design decisions created a large gap between what could have been studied and what was studied. Let’s hope there will be better use of resources next time.

Linear thinking about biological age clocks

This 2020 review by a Hong Kong company’s researchers compared and contrasted measures of biological age:

“More than a dozen aging clocks use molecular features to predict an organism’s age, each of them utilizing different data types and training procedures. We offer a detailed comparison of existing mouse and human aging clocks, discuss their technological limitations and the underlying machine learning algorithms. We also discuss promising future directions of research.

Biomarkers placed on an intuitive plane of Accuracy vs Utility. Bubble size depends on the number of clocks based on a corresponding aging biomarker.

Currently, DNAm [DNA methylation] is the most accurate and the most frequently used biomarker in biohorology. However, it is harder to apply a DNAm clock compared to clocks based on clinical blood tests. Moreover, DNAm marks often take a long time to emerge in response to aging interventions.

Chromatin structure and telomeres, while intriguing, are too labor intensive and error-prone to be practical.”

https://www.sciencedirect.com/science/article/pii/S1568163719302582 “Biohorology and biomarkers of aging: current state-of-the-art, challenges and opportunities”

We think about chronological age linearly. The reviewers hinted at but didn’t directly assess the extent to which techniques such as linear regression may also influence people to think linearly about biological age.

We experience cyclical changes every day (like sleep), month, season, and longer periods. The reviewers didn’t mention techniques that incorporate our cyclical experiences or assess cyclical biological age.

1. The reviewers pointed out some biological age clock linearity flaws:

“Most aging clocks base their BA [biological age] definitions either on CA [chronological age] or mortality risk. Mortality risk in its turn is derived from demographic tables and can be assumed to be a function of CA in most animals, including human.

Thus, aging clocks are ultimately treating CA as a substitute BA with the caveat that deviations from the actual CA signify better or worse physical fitness when compared to age matched controls. Such a design has several flaws.”

2. They pointed out non-linear characteristics of chromosomal telomere length:

“DNA lesions caused by oxidative stress are repaired less efficiently in telomeric regions, which causes frailty and subsequent telomere shortening. Oxidative stress levels may fluctuate due to habitat, life style, inflammatory diseases – factors that do not necessarily represent replicative clock ticking.

Telomere length typically fluctuates within ±2-4% per month. This led scientists to hypothesize that telomere attrition is an oscillatory process.”

Since cell components show cyclical phases, why wouldn’t cells and each higher living structural level likewise demonstrate cyclical phases? That avenue wasn’t explored.

3. They mentioned the non-linearity of epigenetic clocks:

“If an organism’s DNAm profile is not directly linked to the thermodynamic root of aging [entropy] but instead is a downstream product of competing processes, the applicability of DNAm aging clock methodology is at risk. In this case different aging clocks may not be equally good for different experiment settings.

While genetic, pharmacological and dietary interventions with proven effect on life expectancy change the methylation state of the age-associated CpG sites, they do so in different ways. Caloric restriction is more efficient in preventing methylation loss at hypomethylated sites and methylation gain at hypermethylated sites than rapamycin.

These findings imply that DNAm profiles do not simply gravitate towards the average with age and that there is no single pathway through which all aging processes are imbued into an organism’s epigenetic landscape.”

4. Genetic and epigenetic regulatory pathways were presented with linear thinking:

“Protein structures encapsulating DNA and regulating its accessibility (chromatin and histones) have also been shown to change with age. Moreover, DNAm machinery and histone modifications are interlinked and change throughout aging concordantly.

For example, DNA methyltransferases are attracted by the H3K36me mark. With aging it is less tightly regulated, and thus, more sporadic DNAm occurs, which ultimately translates to epigenetic clock ticking.”

An individual’s capability to regulate their own aging phenotype wasn’t addressed, only externally applied “aging interventions.” Diseases were considered chronological-“age-associated.”

Biological aging was neither viewed as a disease nor as an unintended consequence. If these researchers don’t grasp the foundations of their field of study, why do they work in the biological aging field? It isn’t just math.

  • Could this paper reflect one company’s desire to frame arguments in favor of the company’s offered solution?
  • Could this paper reflect a “chronological age is the cause” meme that satisfied organizational imperatives for sponsors like the Buck Institute for Research on Aging?
  • Or could it be that the reviewers had other paradigms?

What do you think?

Humans individually evolve by..?

This 2020 UK evolutionary biology article was part of a “Fifty years of the Price equation” issue:

“Genetic and non-genetic inheritance usually produce a phenotype [the composite of an organism’s characteristics, including its developmental, biophysical, and behavioral traits] through a highly complex developmental process that also relies on many features of the world over which the parents have little, if any, control. As a consequence, the relationship between the phenotypes of parents and offspring, the offspring–parent distribution, can take on many forms and vary from one place or time to another.

The extension of transmission and quantitative genetic models retain the assumption that the relationship between inheritance and phenotypic variation is such that it is sufficient to focus on the transmissibility of inherited variants or additive variance rather than phenotype development.

The concept of heredity as a developmental process is a more significant departure from traditional notions of inheritance. The mechanisms of non-genetic inheritance, such as parental behaviour, do not only affect the parent–offspring resemblance, but also the generation of variation and individual fitness.

Any feature of the parents, including their DNA sequence, physiology and behaviour can carry information about the conditions that the offspring will encounter. That this information content itself must be an evolving property is perhaps most evident when heredity is viewed as a developmental process; a developmental perspective is particularly useful when the aim is to study how the evolutionary process itself is evolving.”

https://royalsocietypublishing.org/doi/full/10.1098/rstb.2019.0366 “Different perspectives on non-genetic inheritance illustrate the versatile utility of the Price equation in evolutionary biology”

This article and the “Fifty years of the Price equation” issue’s other articles had numerous mentions of individual evolution and behavior. They acknowledged “a diversity of perspectives” but I didn’t see my 2015 page’s perspective that it’s up to each individual to mold their own phenotype. In it, the Price equation prompted the question:

“How does a phenotype influence its own change?”

which I applied to a person individually evolving.

The article and the issue’s other articles tinkered with equations, and cited plant, animal, and human studies with frameworks that didn’t include investigating causes for the observed effects. These often wasted resources by providing solutions that addressed symptoms instead of addressing the uninvestigated causes.

For example, I didn’t see any mentions of how an individual’s pain may drive their phenotype. Pain induced by threats to survival are common parts of animal experiments that create and investigate phenotypes of epigenetic responses to stressors.

Regarding possible human applicability, how can a person remedy their undesirable traits and acquire desirable traits without addressing a root cause?

Unlike animals, people can therapeutically resolve underlying causes without the timing, duration, and intensity of efforts being externally determined. A human’s efforts to change their phenotype don’t have to mimic animal studies’ forcible approaches with drugs, etc., directed on someone else’s schedule. Addressing pain may be required for such efforts.

The article also promoted an outdated paradigm of epigenetic transgenerational inheritance:

“The transgenerational stability of some epigenetic states may fall within the same range as the stability of behaviours that are learnt from parents. Quantifying the environmental sensitivity and transgenerational stability of epigenetic variation has emerged as a major research focus over the past decade.”

As explained in Transgenerational epigenetic inheritance of thyroid hormone sensitivity:

“Observing the same phenotype in each generation is NOT required for transgenerational epigenetic inheritance to exist. Animal transgenerational studies have shown that epigenetic inheritance mechanisms may both express different phenotypes for each generation, and entirely skip a phenotype in one or more generations.”

Considering only “transgenerational stability of epigenetic variation” as proof will misinterpret this supporting evidence.

Wander into creativity?

This 2019 US study investigated the context of creative ideas:

“Creative inspiration routinely occurs during moments of mind wandering. Approximately 20% of ideas occurred in this manner.

Although ideas that occurred while participants were both on task and mind wandering did not differ in overall quality, there were several dimensions on which they did consistently differ. Ideas that occurred while mind wandering were reported to be experienced with a greater sense of ‘aha’ and were more likely to involve overcoming an impasse.

The present findings are consistent with the view that spontaneous task-independent mind wandering represents a source of the inventive ideas that individuals have each day. This potential function of mind wandering may help to explain why a mental state that can be associated with significant negative outcomes is nevertheless so ubiquitous.”

“Would you say the idea felt like an ‘aha!’ moment?” and “How creative do you feel the idea was?” were the closest items to emotional measures. “How important do you think this idea is?” and several months later “How important has the idea proven to be overall?” were used to measure importance.

https://labs.psych.ucsb.edu/schooler/jonathan/sites/labs.psych.ucsb.edu.schooler.jonathan/files/pubs/0956797618820626.pdf “When the Muses Strike: Creative Ideas of Physicists and Writers Routinely Occur During Mind Wandering”

I came across this study from its reference in How Productivity Apps Can Make Us Less Productive (And Less Happy).

The study’s design missed opportunities to discover sources of creative ideas and feelings of importance. It focused on effects and intentionally disregarded causes, despite asserting that “mind wandering represents a source of inventive ideas.”

Experiments were subjectively biased for a framework that considered ideas as originating solely from a person’s thinking brain. A framework like Primal Therapy that demonstrated how ideas may arise as defenses against feelings wasn’t considered, although relevant.

Let’s use the finding “Ideas that occurred while mind wandering were more likely to involve overcoming an impasse” as an example for a Primal Therapy framework’s view:

  1. A person who has a seemingly unsolvable work problem probably encounters feelings of helplessness.
  2. Staying busy with tasks can distract them from these feelings.
  3. During times of less cognitive activity, though, these feelings can have more impetus.
  4. The resultant discomfort will trigger ideas to help ward off helpless feelings.

Regarding importance judgments, there are many needs a person develops and tries to satisfy as substitutes for real needs that weren’t fulfilled. I’ve focused on the need to feel important in blog posts such as Your need to feel important will run your life, and you’ll never feel satisfied.

An out-of-date review of epigenetic transgenerational inheritance

This December 3, 2019, French review title was “Transgenerational Inheritance of Environmentally Induced Epigenetic Alterations during Mammalian Development”:

“We attempt to summarize our current knowledge about transgenerational inheritance of environmentally induced epigenetic changes. While the idea that information can be inherited between generations independently of DNA’s nucleotide sequence is not new, the outcome of recent studies provides a mechanistic foundation for the concept.

Systematic resetting of epigenetic marks between generations represents the largest hurdle to conceptualizing epigenetic inheritance. Our understanding of rates and causes of epimutations remains rudimentary.

Environmental exposure to toxicants could promote changes in germline cells at any developmental stage, with more dramatic effects being observed during embryonic germ cell reprogramming. Epigenetic factors and their heritability should be considered during disease risk assessment.”

This review showed an inexplicable lack of thorough research. 2017 was its latest citation of epigenetic transgenerational inheritance studies from Washington State University labs of Dr. Michael Skinner. I’ve curated six of the labs’ 2019 studies!

  1. Transgenerational diseases caused by great-grandmother DDT exposure;
  2. Another important transgenerational epigenetic inheritance study;
  3. The transgenerational impact of Roundup exposure;
  4. Epigenetic transgenerational inheritance mechanisms that lead to prostate disease;
  5. A transgenerational view of the rise in obesity; and
  6. Epigenetic transgenerational inheritance extends to the great-great-grand offspring.

This lack led to – among other items – equivocal statements where current definitive evidence could have been cited. This review was submitted on October 31, 2019, and all above studies were available.

The publisher provided insight into the peer review process via https://www.mdpi.com/2073-4409/8/12/1559/review_report:

  • Peer reviewer 1: “Taking into account that this is not my main area of expertise..Do the authors really believe in that?”
  • Peer reviewer 2 provided a one-paragraph non-review.
  • Peer reviewer 3: “The authors are missing a large sector of what types of environmental factors can influence methylation and do not acknowledge that other sources exist.”

Authors responded with changes or otherwise addressed peer reviewer comments.

https://www.mdpi.com/2073-4409/8/12/1559/htm “Transgenerational Inheritance of Environmentally Induced Epigenetic Alterations during Mammalian Development”

A GWAS meta-analysis of two epigenetic clocks

This 2019 UK human study conducted a meta-analysis of genome-wide association studies of two epigenetic clocks using 13,493 European-ancestry individuals aged between ten and 98 years:

“Horvath-EAA, described in previous publications as ‘intrinsic’ epigenetic age acceleration (IEAA), can be interpreted as a measure of cell-intrinsic ageing that exhibits preservation across multiple tissues, appears unrelated to lifestyle factors, and probably indicates a fundamental cell ageing process that is largely conserved across cell types.

In contrast, Hannum-EAA, referred to in previous studies as ‘extrinsic’ epigenetic age acceleration (EEAA), can be considered a biomarker of immune system ageing, explicitly incorporating aspects of immune system decline such as age-related changes in blood cell counts, correlating with lifestyle and health-span related characteristics, and thus yielding a stronger predictor of all-cause mortality.

The meta-analysis of Horvath-EAA identified ten independent associated SNPs [single nucleotide polymorphisms], doubling the number reported to date, and highlighted 21 genes involved in Horvath-based epigenetic ageing. Four of the ten Horvath-EAA-associated SNPs are mQTL [methylation quantitative trait loci] for CpGs used in the Horvath/Hannum epigenetic clocks. A possible interpretation of this is that the functional mechanism by which these SNPs influence the rate of biological ageing is via altering methylation levels.

Father’s age at death, a rough proxy for lifespan, was nominally significantly correlated with both EAA measures, and parents’ age at death was additionally correlated with Hannum-EAA. Aside from these, genetic correlations with age-related traits were surprisingly few: it is possible that this could reflect an overly conservative correction for the multiple tests carried out, or low statistical power, rather than a genuine lack of correlations.

Genetic correlation analysis should be restricted to GWAS with a heritability Z-score of 4 or more, on the grounds of interpretability and power, so the Horvath-based results particularly should be interpreted with caution.”

A non-apologetic way to explain the above graphic is that NONE of these 218 “health and behavioral traits” were any more associated with the studied genetic measurements than would be expected by chance!

Fervent believers in the GWAS methodology’s capability to exactly predict individual phenotypes eventually become victims of the scientific method. These GWAS researchers griped about “overly conservative correction, or low statistical power” and other predictable shortfalls, and ended a long limitations statement with:

“While we have identified a number of SNPs and genes significantly associated with EAA, including genes already known to be related to ageing, the analyses presented here fall short of providing a mechanistic explanation for how these variants and genes act to influence biological age.”

Outside of beliefs, it’s hard to understand why research money keeps pouring into the GWAS dead end. If these researchers and their employing institution and sponsors want to make a difference in human lives, they need to get busy in other areas.

These researchers were employed by the same institution that couldn’t be bothered to scrape together six more weeks of funds to study the transgenerational damaging effects of acetaminophen – an analgesic available to billions of people – in Epigenetics research that was designed to fall one step short of wonderful.

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008104 “A meta-analysis of genome-wide association studies of epigenetic age acceleration”

PNAS politics in the name of science

This 2019 Germany/Canada human fetal cell study was a Proceedings of the National Academy of Sciences of the United States of America direct submission:

“In a human hippocampal progenitor cell line, we assessed the short- and long-term effects of GC [glucocorticoid] exposure during neurogenesis on messenger RNA expression and DNA methylation profiles. Our data suggest that early exposure to GCs can change the set point of future transcriptional responses to stress by inducing lasting DNAm changes.”

The study’s basic finding was that cells had initial responses to stressors that primed them for subsequent stressors. Since this finding wasn’t new, the researchers tried to make it exciting by applying it to novel contexts that were yet circumscribed by official paradigms.

Hypothesis-seeking associations of human fetal hippocampal cell behaviors with human behaviors were flimsy stretches, as were correlations to placental measurements. These appeared to have been efforts to find headline-making effects.

There wasn’t even a hint of the principle described in Epigenetic variations in metabolism:

“Because of the extreme interconnectivity of cell regulatory networks, even at the cellular level, predicting the impact of a sequence variant is difficult as the resultant variation acts:

  • In the context of all other variants and
  • Their potential additive, synergistic and antagonistic interactions.

This phenomenon is known as epistasis.”

It would have condemned pet models of reality to admit that a cell exists in multiple contexts of other cells with potential additive, synergistic, and antagonistic interactions.

A research proposal to trace a specific cell type’s behaviors – while isolated from their extremely interconnected networks – to trillion-celled human behaviors would be rejected in less-politicized organizations.

Sanctioned speculations manifested in this paper with phrases such as “although not significant..” and “although not directly tested..” The study’s title was probably a disappointment in that it conformed to the study’s evidence.

Involvements of psychiatry departments at the pictured Kings College, Harvard, etc., as part of PNAS entrenched politics, retard advancements of science past approved paradigms.

This is my final curation of PNAS papers.

https://www.pnas.org/content/pnas/early/2019/08/08/1820842116.full.pdf “Glucocorticoid exposure during hippocampal neurogenesis primes future stress response by inducing changes in DNA methylation”

Would you return a lost wallet?

The researchers in this 2019 Swiss/US study intentionally “lost” > 17,000 wallets under experimental conditions:

“We conducted field experiments in 40 countries to examine whether people act more dishonestly when they have a greater economic incentive to do so, and we found the opposite to be true. Citizens were more likely to return wallets that contained relatively larger amounts of money. Neither nonexperts nor professional economists were able to predict this result.

When people stand to heavily profit from engaging in dishonest behavior, the desire to cheat increases but so do the psychological costs of viewing oneself as a thief.”

The study did well in some aspects, including publicity. However:

1. The researchers admitted in the final paragraph:

“Using average reporting rates across countries, we find substantial variation in rates of civic honesty, ranging from 14 to 76%. This variation largely persists even when controlling for a country’s gross domestic product, suggesting that other factors besides a country’s wealth are also at play.”

Yet the paper’s first page contained the above graphic, which used each country’s GDP as a dependent variable! Wasn’t a behavioral economics study of honesty required to present their data honestly, and use factors that were experimentally significant?

2. “Other factors..at play” were relegated to the supplementary materials. The paper was only three-and-a-half pages long, so there was room for further explanations.

Here’s one comment on cultural differences from a Chinese PhD student:

“Biased design. In China (and Asian countries), people seldom use email, and our merit is to leave things untouched (“路不拾遗“:no one picks up lost articles in the street (idiom)).”

3. The study design had nothing to do with avoiding taxes, but three of the four sentences in the paper’s first paragraph did. This impressed as pointless.

https://science.sciencemag.org/content/365/6448/70 “Civic honesty around the globe” (not freely available)

Caloric restriction’s epigenetic effects

This 2019 US review subject was caloric restriction (CR) without malnutrition:

“Cellular adaptation that occurs in response to dietary patterns can be explained by alterations in epigenetic mechanisms such as DNA methylation, histone modifications, and microRNA. Epigenetic reprogramming of the underlying chronic low-grade inflammation by CR can lead to immuno-metabolic adaptations that enhance quality of life, extend lifespan, and delay chronic disease onset.

Short- and long-term CRs produce significant changes in different tissues and across species, in some animal models even with sex-specific effects. Early CR onset may cause a different and even an opposite effect on physiological outcomes in animal models such as body weight.”

https://academic.oup.com/advances/article-abstract/10/3/520/5420411 “Epigenetic Regulation of Metabolism and Inflammation by Calorie Restriction” (not freely available)

1. The review didn’t present evidence to equate survival (left axis) with methylation drift (right axis) per the above graphic. Methylation drift should point in the opposite direction of survival, if anything.

2. No mention was made of the epigenetic clock method of measuring age acceleration, although it’s been available since 2013 and recent diet studies have used it. The sole citation of an age acceleration study was from 2001, which was unacceptable for a review published in 2019.

3. The review provided many cellular-level details about the subject. However, organism-level areas weren’t sufficiently evidenced:

A. Arguments for an effect usually include explanations for no effect as well as for opposite effects. The reviewers didn’t provide direct evidence for why, if caloric restriction extended lifespan, caloric overabundance produced shorter lifespans.

B. Caloric restriction evidence was presented as if only it was responsible for organism-level effects. Other mechanisms may have been involved.

An example of such a mechanism was demonstrated in a 2007 rodent study Reduced Oxidant Stress and Extended Lifespan in Mice Exposed to a Low Glycotoxin Diet which compared two 40%-calorie-restricted diets.

The calories and composition of both diets were identical. However, advanced glycation end product (AGE) levels were doubled in standard chow because heating temperatures were “sufficiently high to inadvertently cause standard mouse chow to be rich in oxidant AGEs.”

The study found that a diet with lower chow heating temperatures increased lifespan and health span irrespective of caloric restriction!

  • The low-AGE calorie-restricted diet group lived an average of 15% longer (>20 human equivalent years) than the CR group.
  • 40% of the low-AGE calorie-restricted diet group were still alive when the last CR group member died.
  • The CR group also had significantly more: 1) oxidative stress damage; 2) glucose and insulin metabolism problems; and 3) kidney, spleen, and liver injuries.