Effects of advanced glycation end products on quality of life and lifespan

This 2018 Chinese review concerned advanced glycation end products (AGE) mobility interventions:

“Only a limited number of studies have focused on measuring the effects of low AGEs levels or AGEs inhibitors on mobility, although many observational human studies and in vitro studies have reported the correlation of AGEs with and the contribution of AGEs to mobility, particular in diseases such as:

  • osteoporosis,
  • cartilage degradation,
  • osteoarthritis and
  • sarcopenia.

There is insufficient information from previous animal and human studies for use as a reference to determine the intervention period. Although serum AGEs levels can be easily affected by a lower AGEs diet or AGEs inhibitors, it may take longer to see the changes in certain organs or tissues, as a result of a reduction in AGEs accumulation.”


“Effect of AGEs on apoptosis signalling. AP-1, activator protein 1; ERK, extracellular signal-regulated protein kinases; IGF-I, insulin-like growth factor I; IL-6, interleukin-6; JAK, Janus kinase; JNK, c-Jun N-terminal kinases; MEK, mitogen-activated protein kinase; NF-κB, nuclear factor kappa B; p38 MAPK, p38 mitogen-activated protein kinase; RAGE, receptor for AGEs; STAT3, signal transducers and activators of transcription 3; TGF-β, transforming growth factor-β”

Citations aren’t validations of the reference’s quality and strength of evidence. This review would have benefited from not citing reviews that contained misrepresentations, such as one mentioned in Wikipedia is a poor source of information on advanced glycation end products (AGEs).

I came across this review as a result of it citing the excellent 2008 rodent study Oral Glycotoxins Determine the Effects of Calorie Restriction on Oxidant Stress, Age-Related Diseases, and Lifespan which found:

“Higher levels of oxidant AGEs in offspring of Reg-F0 dams may be attributable to placental transmission from mothers with high AGE levels. These high intrauterine AGE levels may predispose the offspring to the development of chronic inflammation and diseases in adulthood, such as insulin resistance and diabetes.

Increasing the intake of AGEs in the diet erases the benefits of CR [calorie restriction]. OS [oxidant stress] can be reduced, and healthspan increased, in mice fed a diet that is restricted in the content of AGEs.

The beneficial effects of a CR diet may be partly related to reduced oxidant intake rather than decreased energy intake.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180645/ “Role of advanced glycation end products in mobility and considerations in possible dietary and nutritional intervention strategies”


A drug that countered effects of a traumatizing mother

This 2019 US rodent study concerned transmitting poor maternal care to the next generation:

“The quality of parental care received during development profoundly influences an individual’s phenotype, including that of maternal behavior. Infant experiences with a caregiver have lifelong behavioral consequences.

Maternal behavior is a complex behavior requiring the recruitment of multiple brain regions including the nucleus accumbens, bed nucleus of the stria terminalis, ventral tegmental area, prefrontal cortex, amygdala, and medial preoptic area. Dysregulation within this circuitry can lead to altered or impaired maternal responsiveness.

We administered zebularine, a drug known to alter DNA methylation, to dams exposed during infancy to the scarcity-adversity model of low nesting resources, and then characterized the quality of their care towards their offspring.

  1. We replicate that dams with a history of maltreatment mistreat their own offspring.
  2. We show that maltreated-dams treated with zebularine exhibit lower levels of adverse care toward their offspring.
  3. We show that administration of zebularine in control dams (history of nurturing care) enhances levels of adverse care.
  4. We show altered methylation and gene expression in maltreated dams normalized by zebularine.

These findings lend support to the hypothesis that epigenetic alterations resulting from maltreatment causally relate to behavioral outcomes.”

“Maternal behavior is an intergenerational behavior. It is important to establish the neurobiological underpinnings of aberrant maternal behavior and explore treatments that can improve maternal behavior to prevent the perpetuation of poor maternal care across generations.”

The study authors demonstrated intergenerational epigenetic effects, and missed an opportunity to also investigate transgenerational epigenetically inherited effects. They cited reference 60 for the first part of the above quotation, but that reviewer misused the transgenerational term by applying it to grand-offspring instead of the great-grand-offspring.

There were resources available to replicate the study authors’ previous findings, which didn’t show anything new. Why not use such resources to uncover evidence even more applicable to humans by extending experiments to great-grand-offspring that have no potential germline exposure to the initial damaging cause?

Could a study design similar to A limited study of parental transmission of anxiety/stress-reactive traits have been integrated? That study’s thorough removal of parental behavior would be an outstanding methodology to confirm by falsifiability whether parental behavior is both an intergenerational and a transgenerational epigenetic inheritance mechanism.

Rodent great-grand-offspring can be studied in < 9 months. It takes > 50 years for human studies to reach the transgenerational generation. Why not attempt to “prevent the perpetuation of poor maternal care across generations?”

Isn’t it a plausible hypothesis that humans “with a history of maltreatment mistreat their own offspring?” Isn’t it worth the extra effort to extend animal research to investigate this unfortunate chain?

https://www.nature.com/articles/s41598-019-46539-4 “Pharmacological manipulation of DNA methylation normalizes maternal behavior, DNA methylation, and gene expression in dams with a history of maltreatment”

Linking adult neurogenesis to Alzheimer’s disease

This 2019 Spanish human study compared DNA methylation, chromatin and histone modifications in the hippocampus of deceased Alzheimer’s disease patients with controls:

“A significant percentage of the differentially methylated genes were related to neural development and neurogenesis. It was astounding that other biological, cellular, and molecular processes generally associated with neurodegeneration such as apoptosis, autophagy, inflammation, oxidative stress, and mitochondrial or lysosomal dysfunction were not overrepresented.

The results of the present study point to neurogenesis-related genes as targets of epigenetic changes in the hippocampus affected by AD. These methylation changes might be built throughout life due to external and internal cues and would represent an example of epigenetic interaction between environmental and genetic factors in developing AD.

As an alternative explanation, these epigenetic marks might also represent the trace of DNA methylation alterations induced during early developmental stages of the hippocampus, which would remain as a fingerprint in the larger proportion of hippocampal neurons that are not exchanged. This second hypothesis would link AD to early life stages, in concordance with recent studies that revealed abnormal p-tau deposits (pre-tangles) in brains of young individuals under 30, suggesting AD pathology would start earlier in life than it was previously thought. The influence of the genetic risk for AD has also been postulated to begin in early life, and other AD risk factors may be influenced by in utero environment.”

The study cited references to adult neurogenesis:

“Though strongly related to brain development, neurogenesis is also maintained in the adult human brain, mainly in two distinct areas, i.e., the subventricular zone and the subgranular zone of the dentate gyrus in the hippocampus. There is substantial neurogenesis throughout life in the human hippocampus as it is estimated that up to one third of human hippocampal neurons are subject to constant turnover.

Adult neurogenesis is linked to hippocampal-dependent learning and memory tasks and is reduced during aging. Recent evidence suggests that adult neurogenesis is altered in the neurodegenerative process of AD, but it is still controversial with some authors reporting increased neurogenesis, whereas others show reduced neurogenesis. In the human hippocampus, a sharp drop in adult neurogenesis has been observed in subjects with AD.”

One of the study’s limitations was its control group:

“There was a significant difference in age between controls [12, ages 50.7 ± 21.5] and AD patients [26, ages 81.2 ± 12.1], being the latter group older than the former group. Although we adjusted for age in the statistical differential methylation analysis, the accuracy of this correction may be limited as there is little overlap in the age ranges of both groups.”

https://clinicalepigeneticsjournal.biomedcentral.com/track/pdf/10.1186/s13148-019-0672-7 “DNA methylation signature of human hippocampus in Alzheimer’s disease is linked to neurogenesis”

OCD and neural plasticity

This 2019 New York rodent study investigated multiple avenues to uncover mechanisms of obsessive-compulsive disorder:

“Psychophysical models of OCD propose that anxiety (amygdala) and habits (dorsolateral striatum) may be causally linked. Numerous genetic and environmental factors may reduce striatum sensitivity and lead to maladaptive overcompensation, potentially accounting for a significant proportion of cases of pathological OCD-like behaviors.

Our results indicate that both the development and reversal of OCD-like behaviors involve neuroplasticity resulting in circuitry changes in BLA-DLS and possibly elsewhere.”

The researchers explored two genetic models of OCD, showed why these insufficiently explained observed phenomena, then followed up with epigenetic investigations. They demonstrated how and the degree to which histone modifications and DNA methylation regulated both the development and reversal of OCD symptoms.

The researchers also carelessly cited thirteen papers outside the specific areas of the study to support one statement in the lead paragraph:

“Novel studies propose that modulations in gene expression influenced by environmental factors, are connected to mental health disorders.”

Only one of the thirteen citations was more recent than 2011, and none of them were high-quality studies.

https://www.nature.com/articles/s41598-019-45325-6.pdf “Amelioration of obsessive-compulsive disorder in three mouse models treated with one epigenetic drug: unraveling the underlying mechanism”

Why do we believe obvious lies?

Here are two accounts of this weekend’s news from real journalists, neither of whom are fans of the current US president.

Matt Taibbi of Rolling Stone
“It’s official: Russiagate is this generation’s WMD”

He cited intentional misreporting (lying) multiple times from the New York Times, Washington Post, CNN, Wall Street Journal, MSNBC, Mother Jones; and from NBC, ABC, McClatchy, New Yorker, New York Magazine, Bloomberg, BuzzFeed, Slate, Yahoo, Fortune, Guardian; and from numerous US congressmen and senators. Most of these false stories have still not yet been corrected or retracted.

  • “Recapping: the reporter who introduced Steele to the world (his September 23, 2016 story was the first to reference him as a source), who wrote a book that even he concedes was seen as “validating” the pee tape story, suddenly backtracks and says the whole thing may have been based on a Las Vegas strip act, but it doesn’t matter because Stormy Daniels, etc.
  • When explosive #Russiagate headlines go sideways, the original outlets simply ignore the new development, leaving the “retraction” process to conservative outlets that don’t reach the original audiences.
  • The Russiagate era has so degraded journalism that even once “reputable” outlets are now only about as right as politicians, which is to say barely ever, and then only by accident.
  • Authorities have been lying their faces off to reporters since before electricity! It doesn’t take much investigation to realize the main institutional sources in the Russiagate mess – the security services, mainly – have extensive records of deceiving the media.
  • As noted before, from World War I-era tales of striking union workers being German agents to the “missile gap” that wasn’t (the “gap” was leaked to the press before the Soviets had even one operational ICBM) to the Gulf of Tonkin mess to all the smears of people like Martin Luther King, it’s a wonder newspapers listen to whispers from government sources at all.”

Glenn Greenwald of The Intercept

  1. “Can’t the people who got rich exploiting liberal #Resistance fears by feeding them false conspiracies at least content themselves to their bulging bank accounts from the scam they pulled off & have one day of silence where they don’t try to pretend that they were right all along?
  2. If you’re just going to let stuff like this go – unexamined, unacknowledged, and unaccounted for – don’t expect anyone to be remotely sympathetic to the fact that public trust in big media is nonexistent and politicians benefit by making journalists their enemies.
  3. And just for future reference: documenting the falsehoods, baseless conspiracies, and deceitful narratives being peddled without dissent by the major corporate media isn’t “blogging” or “media criticism.” It’s journalism. It’s reporting. And it’s vital.
  4. Nothing kills journalism worse than cowardly group-think, and it’s worse than ever since they’re congregated in the same places in Brooklyn and the West Coast and petrified of saying anything that makes them unpopular among their peers.
  5. Check every MSNBC personality, CNN law “expert,” liberal-centrist outlets and #Resistance scam artist and see if you see even an iota of self-reflection, humility or admission of massive error.
  6. I wrote this with @GGreenwald in November 2016, warning Russiagate was being used to attack, smear, and censor alternative media. Those blacklisted alternative media ended up being correct about Russiagate – while the corporate media spread actual fake news.
  7. There should be major accountability in the US media and in the intelligence community they united with to drown US political discourse for 2 years straight in unhinged conspiratorial trash, distracting from real issues. That’s what should happen as a first step. But it won’t.”

Statistical inferences vs. biological realities

A 2019 UCLA study introduced a derivative of the epigenetic clock named GrimAge:

“DNAm GrimAge, a linear combination of chronological age, sex, and DNAm-based surrogate biomarkers for seven plasma proteins and smoking pack-years, outperforms all other DNAm-based biomarkers, on a variety of health-related metrics.

An age-adjusted version of DNAm GrimAge, which can be regarded as a new measure of epigenetic age acceleration (AgeAccelGrim), is associated with a host of age-related conditions, lifestyle factors, and clinical biomarkers. Using large scale validation data from three ethnic groups, we demonstrate that AgeAccelGrim stands out among pre-existing epigenetic clocks in terms of its predictive ability for time-to-death, time-to-coronary heart disease, time-to-cancer, its association with computed tomography data for fatty liver/excess fat, and early age at menopause.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366976/ “DNA methylation GrimAge strongly predicts lifespan and healthspan”

A miserable attempt at reporting the study’s findings included angles of superstition, fear-of-the-future, and suspicion-by-spurious-association:

“The research has already captured the attention of the life insurance industry. After all, a solid death date could mean real savings when it comes to pricing policies.

The hope is that if and when legitimate anti-aging drugs are developed, GrimAge could be used to test their effectiveness. In a world with functional anti-aging drugs, “doctors could test [your GrimAge number] and say, ‘You know what, you’re aging too quickly. Take this,'” Horvath said.”

https://onezero.medium.com/a-new-test-predicts-when-youll-die-give-or-take-a-few-years-2d08147c8ea6 “A New Test Predicts When You’ll Die (Give or Take a Few Years)”

A detailed blog post from Josh Mitteldorf provided scientific coverage of the study:

“Methylation sites associated with smoking history predicted how long the person would live more accurately than the smoking history itself. Even stranger, the methylation marks most closely associated with smoking were found to be a powerful indication of future health even when the sample was confined to non-smokers.

The DNAm GrimAge clock was developed in two stages, a correlation of a correlation. Curiously, the indirect computation yields the better result.

Horvath’s finding that secondary methylation indicators are more accurate than the underlying primary indicator from which they were derived is provocative, and calls out for a new understanding.”

https://joshmitteldorf.scienceblog.com/2019/03/05/dnam-grimage-the-newest-methylation-clock “DNAm GrimAge—the Newest Methylation Clock”

When there are logical disconnects in findings like the above, it’s time to examine underlying premises. As noted in Group statistics don’t necessarily describe an individual, an assumption required by statistical analyses is that each measured item in the sample is interchangeable with the next.

This presumption is often false, producing individually inapplicable results. For example, Immune memory vs. immune adaptation included this description of the adaptive immune system:

“To be effective, highly specific immune response requires huge diversity of receptors and antibodies, which is achieved by somatic rearrangement of gene segments. Recombination results in millions of TCR [T cell receptor] and antibody variants able to recognize and neutralize millions of various antigens.”

Standard statistics of millions of T cell receptor and antibody variants won’t represent their individually unique properties. Individual differences are their purpose and benefit to us.

The GrimAge study’s overreach was most apparent in stratifying educational attainment to develop correlations. As mentioned in Does a societal mandate cause DNA methylation? such statistics are poor evidence of each individual’s biological realities.

Neither derivatives of group statistics, nor correlations of correlations, seem to be the techniques needed to understand biological causes of effects. Commentators on the GrimAge study mentioned but glossed over this point:

“It remains a mystery why exactly the epigenetic clocks work, and whether age-related changes in DNA methylation contribute to the cause of aging or are a result of it.”

Immune memory vs. immune adaptation

This 2019 Dutch/German/Romanian perspective aimed for a better understanding of immune systems:

“Based on molecular, immunological, and evolutionary arguments, we propose that innate immune memory is a primitive form of immune memory present in all living organisms, while adaptive immune memory is an advanced form of immune memory representing an evolutionary innovation in vertebrates.

Innate immune responses have the capacity to be trained and thereby exert a new type of immunological memory upon reinfection. The central feature of trained innate immune cells is the ability to mount a qualitatively and quantitatively different transcriptional response when challenged with microbes or danger signals. Evidence supports the convergence of multiple regulatory layers for mediating innate immune memory, including changes in chromatin organization, DNA methylation, and probably non-coding RNAs such as microRNAs and/or long non-coding RNAs.

Two properties of the adaptive immune response are mediated by two fundamentally different types of mechanisms:

  1. The higher magnitude and speed of the response is mediated by epigenetic programming.
  2. The specificity of the response is insured by gene recombination of TCR [T cell receptor] and BCR [B cell receptor] and clonal expansion of specific cell subpopulations upon antigen recognition.

To be effective, highly specific immune response requires huge diversity of receptors and antibodies, which is achieved by somatic rearrangement of gene segments. Recombination results in millions of TCR and antibody variants able to recognize and neutralize millions of various antigens.”

The paper included speculations such as the “Evidence supports..probably non-coding RNAs” quoted above, and the penultimate sentence:

“One can envision that vaccines that are capable of inducing both forms of immune memory at the same time would be more effective.”

100% factual evidence is preferred. The paper’s overall information can only be as accurate as the paper’s least accurate information.

The lead author coauthored A dietary supplement that trains the innate immune system and a study referenced in Eat your oats.

https://www.sciencedirect.com/science/article/pii/S1931312818306334 “Innate and Adaptive Immune Memory: an Evolutionary Continuum in the Host’s Response to Pathogens” (not freely available)