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"Research" that detracted from science
Are overdosed rodent studies relevant to humans?
May 21, 2021 May 22, 2021 gettingwell4 < 0 Detracted from science, Stress	Control group
I partially read more than a dozen studies this week of overdosed rodents producing p < .05 significant results. Net effect was to thwart the purpose of rodent studies – to help humans.
The latest came from search term "SIRT1" "DHEA" 2021 after I read a 2021 study Dehydroepiandrosterone protects against acetaminophen-induced liver damage in rats by upregulation of Bcl-2 and activation of sirt signalling that found:
"The study examined protective effect of exogenous administration of dehydroepiandrosterone (DHEA) against acetaminophen (APAP) -induced liver damage in rats, and tested underlying mechanisms. DHEA prevents APAP-induced liver damage by concomitant upregulation of Bcl-2 and SIRT1-dependent effect."
The daily DHEA dose was 50 mg/kg, which is a (.162 x 50 mg) x 70 kg = 567 mg human equivalent. Eleven times the most frequent human dose of Take responsibility for your one precious life – DHEA. Anyone who took this study's DHEA amount would hurt themself.
The one-time acetaminophen dose was 800 mg/kg which is a (.162 x 800 mg) x 70 kg = 9 grams human equivalent. Someone who took 18 pills of the most frequent 500 mg acetaminophen dose would be attempting suicide.
How does this help humans?
See posts like Problematic rodent sulforaphane studies and Human relevance of rodent sulforaphane studies for further evidence and observations.
Problematic rodent sulforaphane studies
January 5, 2021 January 19, 2021 gettingwell4 < 0 Detracted from science, Epigenetics, Stress	Control group, Genetic factors
I was asked to give an example of Human relevance of rodent sulforaphane studies. I'll use the 2020 Sulforaphane Diminishes the Formation of Mammary Tumors in Rats Exposed to 17β-Estradiol.
1. This study's sulforaphane dose was "100 μmol/kg SFN..gavage regimen on Monday, Wednesday and Friday for 56 weeks." From the October 2019 Broccoli or Sulforaphane: Is It the Source or Dose That Matters? "Allometric scaling uses the correction factor for rat doses 0.162" and this graphic:
Interpreting the human-relevant range:
Interpreting that 8% of the rodent studies were clinically relevant to human sulforaphane doses as a lower boundary (1.43 µmol / kg) and tolerable to humans as an upper boundary (4 µmol / kg):
A human equivalent of this study's dose is (100 μmol/kg x .162) = 16.2 µmol / kg. See the original blog post for a study showing that a majority of both treatment and control group subjects will refuse and stop with sulforaphane doses less than half of this study's human equivalent.
2. From Week 28, "The maximum lifespan for rats and humans were set to 3.8 years and 122.5 years, respectively." A human-equivalent multiplication factor that can be applied to a rat post-development time period is 122.5 / 3.8 = 32.2.
Assuming this study's subjects could achieve maximum lifespan, a human equivalent of 56 weeks is (56 x 32.2) ≈ 1,803 weeks, or ≈ 34.7 years.
3. Let's assert that the main purpose of animal studies is to help humans.
Was it possible for this study to achieve this goal when it used intolerable human-equivalent sulforaphane doses for a period equivalent to over three decades of our lives?
Yet its Discussion section proposed that it's useful for human guidance on:
Breast cancer in premenopausal and postmenopausal women;
Hormone status;
Phospholipids for cellular health and homeostasis;
Serum free fatty acids and triglycerides; and
Lipid metabolism and DNA damage.
4. These researchers definitely knew what this study was going to do. A coauthor of the above referenced 2019 paper was also a coauthor of this study, who "conceived the original study design and supervised the project."
Why did they do it? The coauthor's shared apology – published in the October 2019 paper – for these types of studies was:
"Animal studies have not delivered all that might be expected of them. Pre-clinical experimentalists have not thought carefully about the selection of dose (or route) and its relevance to clinical utility.
Authors of this review have contributed to this dose skewing."
This study was published in July 2020.
It wasn't just a waste of resources. It detracted from science because people won't recognize that its findings are inapplicable to humans.
A research train wreck
October 13, 2020 October 15, 2020 gettingwell4 < 0 Detracted from science	Control group
I try to highlight research that advances science. Please humor a momentary break.
This 2020 study Effects of cooking methods on total isothiocyanate yield from cruciferous vegetables simulated microwaving broccoli to 210° C (410° F). These researchers knew or should have known that myrosinase inactivates at moderate temperatures, given studies published last century such as this with its "Thermal inactivation proceeded in the temperature range 30−60° C" finding. Without an active enzyme, no isothiocyanates are produced from cooking broccoli.
Incredibly, these researchers proved they knew their study detracted from science by citing Microwave broccoli to increase sulforaphane levels. That study found destructive effects on sulforaphane at temperatures above 60° C (140° F):
The sulforaphane (SFR) amount at HL70° on the right (broccoli heated to 70° C with a 950 W microwave operated on full power) was significantly less than uncooked broccoli (control) on the left!
"This work was supported by the National Cancer Institute."
I haven't found words to correspond with the coauthors. Egregious errors speak for themselves.
Politically correct about erucic acid and broccoli seeds
July 20, 2020 April 18, 2021 gettingwell4 < 0 Detracted from science
To follow up Caution on broccoli seed erucic acid content? this 2020 German review sympathetically analyzed government overreach on erucic acid contents in several foods:
"We measured exemplarily samples of rapeseed, mustard, further Brassicaceae and used the data to discuss possible consequences for consumers, producers and the food sector. This data was supplemented with possible analytical problems.
The new and lower erucic acid level in the EU is anticipated but will increase the need of an efficient control system by producers and food processors in order to avoid violations of erucic acid limit values and sale bans. The new proposed legislation will likely prompt some producers to reformulate their recipes, which can be achieved by lowering the fat content or by moving to mustard seeds with lower erucic acid content.
The amount of erucic acid in fish should not be neglected."
https://www.sciencedirect.com/science/article/pii/S235236462030002X "Erucic acid in Brassicaceae and salmon – An evaluation of the new proposed limits of erucic acid in food" (not freely available)
The paper didn't measure erucic acid percentages of total fatty acids in broccoli seeds. Also noticeably absent were analyses of animal studies performed a long time ago that formed the bases of current government actions.
Nothing to see here, move along. Much more effort was put into creating new health hazards for consumers, as if we should now be required to worry about eating salmon.
The 2017 position paper establishing erucic acid limits was excessively cited twelve times, such as for:
"Likewise, broccoli seeds were high in erucic acid but this fatty acid was not detected in edible parts of the vegetable. Hence, intake of erucic acid via these vegetables seems to be irrelevant."
I mentioned problems in the poorly-evidenced 2002 study cited by this position paper. That researcher couldn't be bothered to use just one broccoli cultivar for only three measurements, or disclose broccoli sprout age. But apparently it's a fait accompli, elevated to an indisputable fact.
Despite many technical details, the current paper was politics. It detracted from science, with a cover story "in favor of consumer protection." Poorly-evidenced assertions are not science.
These researchers descended further into advocacy with "analysis" beginning with:
"Imagine (cruciferous) vegetables having an erucic acid content of 50% in the lipids."
They did cause me to "imagine" eating hot dogs with mustard. But maybe that's because baseball season is finally starting?
These vendors of broccoli seed powder don't seem concerned about disclosing erucic acid content. What do you think?
Using oxytocin receptor gene methylation to pursue an agenda
December 18, 2019 November 8, 2020 gettingwell4 < 0 Detracted from science, Amygdala, Brain development, Brain hemispheres, Cerebrum, Cortisol, Epigenetics, Hippocampus, Hypothalamus, Limbic system, Memory, Neurochemicals, Oxytocin, Stress, Vasopressin	Brain neurons, Critical period, DNA methylation, Happiness, Infants, Language development, Neural plasticity, Prefrontal cortex, Unconscious feelings, Unconscious memories
A pair of 2019 Virginia studies involved human mother/infant subjects:
"We show that OXTRm [oxytocin receptor gene DNA methylation] in infancy and its change is predicted by maternal engagement and reflective of behavioral temperament."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6795517 "Epigenetic dynamics in infancy and the impact of maternal engagement"
"Infants with higher OXTRm show enhanced responses to anger and fear and attenuated responses to happiness in right inferior frontal cortex, a region implicated in emotion processing through action-perception coupling.
Infant fNIRS [functional near-infrared spectroscopy] is limited to measuring responses from cerebral cortex. It is unknown whether OXTR is expressed in the cerebral cortex during prenatal and early postnatal human brain development."
https://www.sciencedirect.com/science/article/pii/S187892931830207X "Epigenetic modification of the oxytocin receptor gene is associated with emotion processing in the infant brain"
Both studies had weak disclosures of limitations on their findings' relevance and significance. The largest non-disclosed contrary finding was from the 2015 Early-life epigenetic regulation of the oxytocin receptor gene:
These results suggest that:
Blood Oxtr DNA methylation may reflect early experience of maternal care, and
Oxtr methylation across tissues is highly concordant for specific CpGs, but
Inferences across tissues are not supported for individual variation in Oxtr methylation.
That rat study found that blood OXTR methylation of 25 CpG sites couldn't accurately predict the same 25 CpG sites' OXTR methylation in each subject's hippocampus, hypothalamus, and striatum (which includes the nucleus accumbens) brain areas. Without significant effects in these limbic system structures, there couldn't be any associated behavioral effects.
But CpG site associations and correlations were deemed good in the two current studies because they cited:
"Recent work in prairie voles has found that both brain- and blood-derived OXTRm levels at these sites are negatively associated with gene expression in the brain and highly correlated with each other."
https://www.sciencedirect.com/science/article/pii/S0306453018306103 "Early nurture epigenetically tunes the oxytocin receptor"
The 2018 prairie vole study – which included several of the same researchers as the two current studies – found four nucleus accumbens CpG sites that had high correlations to humans. Discarding one of these CpG sites allowed their statistics package to make a four-decimal place finding:
"The methylation state of the blood was also associated with the level of transcription in the brain at three of the four CpG sites..whole blood was capable of explaining 94.92% of the variance in Oxtr DNA methylation and 18.20% of the variance in Oxtr expression."
Few limitations on the prairie vole study findings were disclosed. Like the two current studies, there wasn't a limitation section that placed research findings into suitable contexts. So readers didn't know researcher viewpoints on items such as:
What additional information showed that 3 of the 30+ million human CpGs accurately predicted specific brain OXTR methylation and expression from saliva OXTR methylation?
What additional information demonstrated how "measuring responses from cerebral cortex" although "it is unknown whether OXTR is expressed in the cerebral cortex" provided detailed and dependable estimates of limbic system CpG site OXTR methylation and expression?
Was the above 25-CpG study evidence considered?
Further contrast these three studies with a typical, four-point, 285-word limitation section of a study like Prenatal stress heightened adult chronic pain. The word "limit" appeared 6 times in that pain study, 3 times in the current fNIRS study, and 0 times in the current maternal engagement and cited prairie vole studies.
Frank interpretations of one's own study findings to acknowledge limitations is one way researchers can address items upfront that will be questioned anyway. Such analyses also indicate a goal to advance science.
A strawman argument against epigenetic clocks
November 14, 2019 September 25, 2021 gettingwell4 < 0 Detracted from science, Epigenetics, Immune system, Stress, Telomeres	Brain neurons, DNA methylation, Genetic factors
This 2019 review of epigenetic clocks by Washington cancer researchers ignored the elephant in the room: Their epigenetic drift paradigm is generally inapplicable to humans because the vast majority of our cells don't divide/proliferate. They repeatedly returned to an argument for randomness as a cause for aging and disease:
"A time-dependent stochastic event process, like epigenetic drift, could lead to cancer formation through the accumulation of random epigenetic alterations that, through chance, eventually alter epigenetic driver gene expression leading to a clone of cells destined to become cancer.
It is plausible that the stochastic process inherent in epigenetic drift can induce aberrant methylation events that accumulate in normal cells and eventually induce cancer formation.
Epigenetic drift relates to a biological process that changes the DNA methylome with age via stochastic gains or losses of DNA methylation. Epigenetic drift can be understood in terms of errors in DNA methylation maintenance during DNA-replication.
The phenomenon of (epi)genetic drift is generally associated with phenotypic neutrality.
For patients who develop cancer around age 80, the most likely initiation time for the founder adenoma cell is predicted to be very early in life, roughly between the ages 15 to 20 years. This unexpected and provocative finding suggests that the optimal age-range for prevention of colorectal cancer may be in adolescence and early adulthood (and ideally through lifelong) dietary and lifestyle interventions."
The reviewers' strawman arguments intentionally mischaracterized aspects of the epigenetic clock:
1. The epigenetic clock founder's actual view on aging was in The epigenetic clock theory of aging:
"The proposed epigenetic clock theory of ageing views biological ageing as an unintended consequence of both developmental programmes and maintenance programmes, the molecular footprints of which give rise to DNAm age estimators."
The reviewers omitted this intrinsic view of aging, which didn't fit into the above graphic.
2. Another misrepresentation was:
"In contrast to epigenetic clocks, epigenetic drift refers to a stochastic process that involves both gains and losses of the methylation state of CpG dinucleotides over time."
A reader of the original 2013 epigenetic clock study would understand that epigenetic clocks measure "both gains and losses of methylation" as in:
"The 193 positively and 160 negatively correlated CpGs get hypermethylated and hypomethylated with age, respectively."
3. These reviewers omitted recent epigenetic clock significant developments. For example, there was no mention of the GrimAge study, although it was published before this review was submitted.
4. Epigenetic drift as the cause of aging and disease has abundant contrary evidence. These reviewers tossed in a little toward the end of their directed narrative:
"We found only a small number of drift-related CpG island-gene pairs for which drift correlated positively and significantly with gene expression.
The functional consequences of epigenetic drift need to be further elucidated."
However, they never acknowledged the elephant in the room!
https://cancerres.aacrjournals.org/content/early/2019/11/06/0008-5472.CAN-19-0924 "Epigenetic aging: more than just a clock when it comes to cancer" (not freely available)
Restrict information in the name of science?
November 4, 2019 September 6, 2020 gettingwell4 < 0 Detracted from science, Beliefs, Cerebrum	Reputations
A Stanford researcher was annoyed that we live in the 21st century, and advocated we return to previous centuries' information-flow check valves of wise old men. No doubt the publishers of and subscribers to the Journal of the American Medical Association applauded the same old tired prescription.
Ten instances of the word "should" in the final two paragraphs provided ample evidence of the paper's intent. Mirroring the current political climate – projecting – accusations made of others were items the accusers were guilty of themselves, such as:
"When these scientists act as investigators in the hundreds of observational studies that they publish, or as editors and peer reviewers in evaluating submissions from others, would they tolerate publishing analyses and funding proposals that might contradict their belief system?"
https://jamanetwork.com/journals/jama/fullarticle/2753533 "Neglecting Major Health Problems and Broadcasting Minor, Uncertain Issues in Lifestyle Science"
One of the paper's references included an informative graphic:
"A histogram of the total number of rumor cascades in our data across the seven most frequent topical categories."
https://science.sciencemag.org/content/359/6380/1146 "The spread of true and false news online"
I'll borrow from the curation of another Stanford paper Online dating cuts out the middlemen in conclusion:
"Are there examples where it wouldn't potentially improve a person's life to choose their information sources? Friends, family, and other social groups – and religious, educational, and other institutions – have had their middlemen/guarantor time, and have been found lacking.
Make your own choices for your one precious life."
Because..Harvard?
October 25, 2019 October 31, 2019 gettingwell4 < 0 Detracted from science, Epigenetics
This 2019 Harvard review entitled "Transgenerational epigenetic inheritance: from phenomena to molecular mechanisms" DETRACTED from science. Readers would become less-informed on the subject due to poorly-researched statements such as:
"Non-Mendelian inheritance, termed transgenerational epigenetic inheritance,"
which wasn't an adequate definition of the transgenerational epigenetic inheritance term.
Contributing to the paper's misdirection was the omission of Dr. Michael Skinner from any of the 349 cited references. Hard to believe that ignoring his research wasn't intentional, since a PubMed "transgenerational" search sorted by Best Match displayed Dr. Skinner as author or coauthor in 3 of the first 20 results:
Endocrine disruptors in 2015: Epigenetic transgenerational inheritance;
Environmentally induced epigenetic transgenerational inheritance of disease; and
Epigenetic transgenerational actions of endocrine disruptors and male fertility.
The abstract asserted:
"How this epigenetic information escapes the typical epigenetic erasure that occurs upon fertilization and how it regulates behavior is still unclear."
However, Another important transgenerational epigenetic inheritance study – published well before the current paper – was one of Dr. Skinner's Washington State University lab studies that CLEARLY demonstrated contrary evidence.
Who benefits from hijacking a scientific term and ignoring groundbreaking research?
Why did the two editors approve for publication a paper with obvious omissions and egregious errors? Because..Harvard?
https://www.sciencedirect.com/science/article/abs/pii/S0959438818302204 "Transgenerational epigenetic inheritance: from phenomena to molecular mechanisms" (not freely available)
Wikipedia is a poor source of information on advanced glycation end products (AGEs)
July 14, 2019 September 11, 2019 gettingwell4 < 0 Detracted from science, Beliefs, Cerebrum, Epigenetics, Immune system, Stress
A link to Wikipedia is usually on the first page of search results. The Wikipedia post on AGEs lacks the evidence that a reader may infer from its text.
For example, the second paragraph of the AGEs post, Dietary Sources, contained the following text and references:
"However, only low molecular weight AGEs are absorbed through diet, and vegetarians have been found to have higher concentrations of overall AGEs compared to non-vegetarians. [4]
Therefore it is unclear whether dietary AGEs contribute to disease and aging, or whether only endogenous AGEs (those produced in the body) matter. [5]
This does not free diet from potentially negatively influencing AGE, but implicates dietary AGE may be less important than other aspects of diet that lead to elevated blood sugar levels and formation of AGEs. [4] [5]"
[4] https://www.sciencedirect.com/science/article/pii/S0278691513004444 "Advanced glycation end products in food and their effects on health" (not freely available) 2013 Denmark.
Please note on this linked page that a German researcher took the time to correct one bias of the Danish reviewers, citing evidence from his studies that:
"The deleterious effects of food-derived AGEs in subjects with type 2 diabetes mellitus are proven."
[5] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257625 "Dietary Advanced Glycation End Products and Aging" 2010 US.
Both of these references were reviews.
Unlike study researchers, reviewers aren't bound to demonstrate evidence from tested hypotheses. Reviewers are free to:
Express their beliefs as facts;
Over/under emphasize study limitations; and
Disregard and misrepresent evidence as they see fit.
Reviewers also aren't obligated to make post-publication corrections for their errors and distortions. For example, the Danes didn't correct their review with any findings the German researcher presented.
As such, reviews can't be cited for reliable evidence.
A sample of other problems with each of the Wikipedia sentences:
1. "However, only low molecular weight AGEs are absorbed through diet, and vegetarians have been found to have higher concentrations of overall AGEs compared to non-vegetarians. [4]"
The first part of sentence 1 came from the review's abstract:
"Only LMW AGEs..may be absorbed from the gut and contribute to the body burden of AGEs."
But the reviewers didn't support their abstract's statement with direct evidence from any study!
2. "Therefore it is unclear whether dietary AGEs contribute to disease and aging, or whether only endogenous AGEs (those produced in the body) matter. [5]"
The "therefore" of sentence 2 was misplaced. Sentence 1 didn't attempt to explain whether "dietary AGEs contribute to disease and aging" or "only endogenous AGEs matter."
Since sentence 2 wasn't a consequence of sentence 1, the Wikipedia contributor(s) needed to support sentence 2 with evidence. Citing an "unclear" 2010 reference [5] ignored dozens of studies that provided better clarity.
3. "This does not free diet from potentially negatively influencing AGE, but implicates dietary AGE may be less important than other aspects of diet that lead to elevated blood sugar levels and formation of AGEs. [4] [5]"
Wikipedia contributors tend to cite irrelevant references rather than get flagged with "citation needed." The value judgment of sentence 3 was an example of this intentionally misleading masquerade.
"Dietary AGE may be less important.." wasn't unequivocally supported by studies referenced in either review, and didn't represent an authoritative body of evidence. Contrast those weasel words with:
Good job, Wikipedia contributors! You used lower-quality reviews to promote misunderstandings that DETRACTED from science.
Wikipedia's premise is that since the group knows more about any subject than does any individual, everyone is entitled to contribute. The results are usually incoherent narratives that often substitute opinions for evidence.
The second paragraph of the Exogenous section of the Wikipedia glycation post provided an example:
Assertions of the first and third sentences needed citations. Did the contributor(s) think these would be unexamined?
Someone contributed a cancer reference as the fourth sentence, although it had little to do with the preceding sentences.
The fifth sentence was informative on exogenous glycations and AGEs. An editor would have removed "recently" and "recent" though, because the cited source was dated 2005.
Infant DNA methylation and caregiving
June 13, 2019 June 13, 2019 gettingwell4 < 0 Detracted from science, Brain development, Cortisol, Epigenetics, Neurochemicals, Stress	Critical period, DNA methylation, Infants
This 2019 US human study attempted to replicate findings of animal studies that associated caregiver behavior with infant DNA methylation of the glucocorticoid receptor gene:
"Greater levels of maternal responsiveness and appropriate touch were related to less DNA methylation of specific regions in NR3c1 exon 1F, but only for females. There was no association with maternal responsiveness and appropriate touch or DNA methylation of NR3c1 exon 1F on prestress cortisol or cortisol reactivity. Our results are discussed in relation to programming models that implicate maternal care as an important factor in programing infant stress reactivity."
The study had many undisclosed and a few disclosed limitations, one of which was:
"Our free-play session, while consistent with the length of free-play sessions in other studies, was short (5 min). It is unclear whether a longer length of time would have yielded significant different maternal responsiveness and appropriate touch data."
The final sentence showed the study's purpose was other than discovering factual evidence:
"Following replication of this work, it could ultimately be used in conjunction with early intervention, or home-visiting programs, to measure the strength of the intervention effect at the epigenetic level."
https://onlinelibrary.wiley.com/doi/full/10.1002/imhj.21789 "DNA methylation of NR3c1 in infancy: Associations between maternal caregiving and infant sex" (not freely available)
Burying human transgenerational epigenetic evidence
January 4, 2019 October 16, 2021 gettingwell4 < 0 Detracted from science, Beliefs, Cerebrum, Epigenetics	Control group, Embryo development, Inherited disease
The poor substitutes for evidence in this 2018 US study guaranteed that human transgenerational epigenetically inherited effects wouldn't be found in the generations that followed after prenatal diethylstilbestrol (DES) exposure:
"A synthetic, nonsteroidal estrogen, DES was administered to pregnant women under the mistaken belief it would reduce pregnancy complications and losses. From the late 1930s through the early 1970s, DES was given to nearly two million pregnant women in the US alone.
Use of DES in pregnancy was discontinued after a seminal report showed a strong association with vaginal clear cell adenocarcinoma in prenatally exposed women. A recent analysis of the US National Cancer Institute (NCI) DES Combined Cohort Follow-up Study showed elevated relative risks of twelve adverse health outcomes.
We do not have sufficient data concerning the indication for DES in the grandmother to determine whether adverse pregnancy outcomes in the third generation might resemble those of their grandmothers. Fourth generation effects of prenatal exposures in humans have not been reported."
https://www.sciencedirect.com/science/article/pii/S0890623818304684 "Reproductive and Hormone-Related Outcomes in Women whose Mothers were Exposed in utero to Diethylstilbestrol (DES): A Report from the US National Cancer Institute DES Third Generation Study" (not freely available)
This study had many elements in common with its poor-quality reference [25] "Transgenerational effects of prenatal exposure to the 1944–45 Dutch famine" which is freely available at https://obgyn.onlinelibrary.wiley.com/doi/full/10.1111/1471-0528.12136.
That study's Methods section showed:
Its non-statistical data was almost all unverified self-reports by a self-selected sample of the F2 grandchildren, average age 37.
No detailed physical measurements or samples were taken of the F2 grandchildren, or of their F1 parents, or of their F0 grandparents, all of which are required as baselines for any transgenerational epigenetic inheritance findings.
No detailed physical measurements or samples were taken of the F3 great-grandchildren, which is the generation that may provide transgenerational evidence if the previous generations also have detailed physical baselines.
That study's researchers drew enough participants (360) such that their statistics package allowed them to impute and assume into existence a LOT of data. But the scientific method constrained them to make factual statements of what the evidence actually showed. They admitted:
"In conclusion, we did not find a transgenerational effect of prenatal famine exposure on the health of grandchildren in this study."
The current study similarly used the faulty methods 1-3 above to produce results such as:
"We do not have sufficient data concerning the indication for DES in the [F0] grandmother to determine whether adverse pregnancy outcomes in the [F2] third generation might resemble those of their grandmothers.
Fourth [F3] generation effects of prenatal exposures in humans have not been reported."
Zero studies of probably more than 10,000,000 F3 great-grandchildren of DES-exposed women just here in the US?
Who is against funding these studies? Who is afraid of what such studies may find?
One plausible hypothesis of these human studies would be of inherited effects that skipped generations! The rodent studies Epigenetic transgenerational inheritance mechanisms that lead to prostate disease and Epigenetic transgenerational inheritance of ovarian disease found inherited diseases that didn't manifest until the F3 great-grand offspring:
The F3 generation can have disease while the F1 and F2 generations do not.
Ancestral exposure to toxicants is a risk factor that must be considered in the molecular etiology of ovarian disease.
For the current study:
What could be expected from a study design that didn't include F3 women and men, which is the only generation that didn't have direct DES exposure?
What a nonsensical study design to permit NON-evidence like educational level!
Human studies of possible intergenerational and transgenerational epigenetic inheritance are urgently needed. There will be abundant evidence to discover if researchers will take their fields seriously.
Hijacking the epigenetic clock paradigm
August 25, 2018 September 14, 2018 gettingwell4 < 0 Detracted from science, Epigenetics, Telomeres	DNA methylation
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)
Going off the rails with the biomarker paradigm
August 16, 2018 September 6, 2018 gettingwell4 < 0 Detracted from science, Acetylcholine, Dopamine, Epigenetics, Hippocampus, Limbic system, Memory, Neurochemicals	Brain neurons, Control group, Critical period, DNA methylation, Neural plasticity
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 – published by the US Centers for Disease Control as 88.8 kg – to compare the study's dosages with human equivalents:
Nicotine at "12.6mg/kg/day" x 88.8 kg = 1119 mg. The estimated lower limit of a lethal dose of nicotine has been reported as between 500 and 1000 mg!
Choline at "9g/kg" x 88.8 kg = 799 g. The US National Institutes of Health published the Tolerable Upper Intake Levels for Choline as 3.5 g!!
Neither of these dosages are even remotely connected to human realities:
The human-equivalent dosage of nicotine used in this study would probably kill an adult human before the end of 12 days.
What effects would an adult human suffer from exceeding the choline "Tolerable Upper Intake Level" BY 228 TIMES for 30 days?
Isn't the main purpose of animal studies to help humans? What's the justification for performing animal studies simply to promote an agenda?
A funding source of this study was National Institute on Drug Abuse (NIDA) Identification of Biomarkers for Nicotine Addiction award (T-DA-1002 MG). Has the biomarker paradigm been institutionalized to the point where research proposals that don't have biomarkers as goals aren't funded?
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)
A book review of "Neuroepigenetics and Mental Illness"
August 12, 2018 October 26, 2019 gettingwell4 < 0 Detracted from science, Brain development, Epigenetics, Stress	Antidepressants, Embryo development
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
"Chapter Eleven: Using Epigenetic Tools to Investigate Antidepressant Response" https://www.sciencedirect.com/science/article/pii/S1877117318300711
"Chapter Twelve: Transgenerational Epigenetics of Traumatic Stress" https://www.sciencedirect.com/science/article/pii/S187711731830053X
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 advancing science. The meme is that there are adequately evidenced transgenerational epigenetic inheritance human results.
As 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 that it's already been 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 one example of the poor substitutes for evidence that propagators of this transgenerational meme use to pronounce human transgenerational epigenetic inheritance a fait accompli. Researchers supporting the meme and its funding pipeline most certainly know that not only this one example, but also ALL human transgenerational epigenetic inheritance studies:
"Lack clear "cause and effect" association, mechanistic explanations or germline assessment."
Lack of scientific integrity is one reason why such human research hasn't been undertaken with the urgency it deserves. Propagating this meme is unethical, and adversely affects anyone who values evidence-based research.
A disturbance in the paradigm of child abuse
June 7, 2018 December 31, 2020 gettingwell4 < 0 Detracted from science, Brain development, Epigenetics, Immune system, Stress	DNA methylation, Embryo development, Genetic factors, Inherited disease
The principal way science advances is through a principle Einstein expressed as:
"No amount of experimentation can ever prove me right; a single experiment can prove me wrong."
The scientific community and 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 evidence didn't confirm current biases. I curated one of these studies in DNA methylation and childhood adversity.
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."
Commentators – one of whom was a coauthor of Manufacturing PTSD evidence with machine learning, – went on to protect their territory. Nevermind these two studies' advancement of science that didn't coincide with commentators' vested interests.
My main concern with the curated study was that although child subjects had been studied at ages 5, 7, 10, 12, and 18, parents had never been similarly evaluated! Those researchers passed up an opportunity to develop parents as a F0 generation for understanding possible human transgenerational inherited epigenetic causes and effects.
That study focused on the children's intergenerational epigenetic effects. However, animal studies have often demonstrated transgenerational effects that skip over F1 generation children! For example:
Transgenerational pathological traits induced by prenatal immune activation found a F2 grandchild and F3 great-grandchild phenotype of impaired sociability, abnormal fear expression and behavioral despair – effects that weren't present in F1 children;
A self-referencing study of transgenerational epigenetic inheritance found histone modifications in the F3 generation that weren't found in F1 and F2 generations; and
A study not cited in – but completely appropriate for – The lack of oxygen's epigenetic effects on a fetus found heart disease effects in the F1 generation that were different from the heart disease effects found in F2 and F3 generations.
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)
A rejuvenation therapy and sulforaphane