Epigenetics and the Direction of Anti-Aging Science

Dear Readers –

It’s been a deeply gratifying year for me.  Twenty years ago, I first started writing that aging is something the body does to itself, a body function, rather than deterioration or loss of function.  Journals would not even send my submission out for peer review.  Journal of Theoretical Biology sent me the considered opinion of their anonymous reviewer, “JTB shouldn’t touch this topic with a ten-foot pole.”  The conflict with prevailling evolutionary theory was just too deep.

But in the interim, the evidence has continued to pile up, and many medical researchers have taken the message to heart in a practical way, setting aside the evolutionary question and just pursuing approaches that seem to work.  The most promising developments in anti-aging medicine involve changing the signaling environment rather than trying to “fix what goes wrong” with the body.

My popular book exploring the evolutionary origins of aging (and implications for medical science) came out in June, and an academic version of the same content came out in October.  Gandhi taught me,

“First they ignore you…
then they laugh at you…
then they fight you…
then you win.”

The paradigm of programmed aging passed this year from stage 2 to stage 3, with prominent articles arguing against the possibility of programmed aging [Kirkwood, de Grey, Vijg & Kennedy].  Current Aging Sciences devoted a full issue to the question.  I welcome the discussion.  This is a debate that colleagues and I have sought to initiate for many years.  There are powerful theoretical arguments on one side, and diverse empirical observations on the other.  The scientific community will eventually opt for empiricism, but not until theory digs in its heels and fights to the death.  A basic principle of evolution is at stake, and many theorists will rise to defend the basis of their life work; but a re-evaluation of basic evolutionary theory is long overdue.

The idea that fitness consists in reproducing as fast as possible is no longer tenable.  For plants, this may be approximately true.  But animal populations cannot afford to reproduce at a pace faster than the base of their food chain can support.  Animals that exploit their food supply unsustainably will starve their own children, and there is no evolutionary future in that.  This is a principle that links together entire ecologies, and the foundation of evolutionary theory will have to be rewritten to take it into account.

 

The Programmed Aging Paradigm: Is it a Cause for Optimism in the Quest for Extended Human Life?

For many years, I put forward the argument that programmed aging means there are genes that serve no other purpose than to hasten our death, and that medical research should be targeting the products of those genes.  (Once a pathway has been identified, pharmaceutical science knows well how to block it with engineered drugs, like beta blockers and MAO inhibitors and serotonin re-uptake inhibitors.)

But in recent years, epigenetics has eclipsed genetics as the major theme in molecular biology.  Everything that happens in the body is determined by which genes are expressed where and when.  The vast majority of our DNA is devoted not to coding of proteins but to promoter and repressor regions that control gene expression with exquisite subtlety.

There has been a growing recognition of aging as an epigenetic program.  As we get older, genes that protect us are dialed down, and genes for inflammation and apoptosis are dialed up so high that healthy tissue is being destroyed.  Many epigenetic scientists have discovered this, and they find it natural to see aging as a programmed phenomenon.  (Most have never been to graduate courses in evolutionary science, where they would have been indoctrinated into the perspective of the selfish gene.)

At first blush, it seems that an epigenetic program is just as amenable to pharmaceutical intervention as a genetic program.  A few years ago, I wrote about transcription factors as the key to aging.  Transcription factors bind to DNA and turn whole suites of genes on and off in a coordinated way.  If we can restore a youthful transcription environment in an older animal or human, the body knows how to repair damage and re-create a younger self.  The model I had in mind was based on a small number of powerful transcription factors controlling expression of a much larger number of genes, controlling a yet larger population of metabolites.

I no longer believe in this model.

This summer, I had a chance to work in a worm genetics lab and consult closely with people who know the experimental details.  I learned that there is no clear line between functional proteins and transcription factors, that many proteins have multiple functions, and that metabolites feed back to control gene expression.  Instead of a pyramid, I should think of a web of causes and effects.

The entire system is primed for homeostasis, meaning that it responds to any intervention, seeking to move the system back toward its previous state.  Of course, it is this capacity for recovery that makes life robust; but it also means that there is no “command central” which can be tweaked to move the whole system at once toward a desired state.

I still believe that there are one or more aging clocks that inform the body of an age-appropriate metabolic state, and synchronize the aging of different systems.  Telomere length is one such clock.  If we can reset an aging clock, the body will repair and clean itself up.  If we can reset several clocks, the body may be able to restore itself to a younger state.  But I recognize the possibility that the clock is diffused through the detailed epigenetic status of a trillion cells, and may be beyond the reach of foreseeable technology.

A few years ago, Steve Horvath of UCLA gave us the most explicit picture of an aging clock.  He found it in one particular epigenetic marker: the pattern of DNA methylation.  The Horvath clock is distributed over 353 sites.  This is a clock that can be read for any given cell, but can it be changed or adjusted in each of the body’s trillions of cells?  The prospect is daunting, and we do not yet know how to go about it.  2016 saw the first use of CRISPR technology for therapy in a living human.  CRISPR could, in principle, be used to alter gene expression, one gene at a time.  To re-regulate the expression of 353 genes in one treatment would probably require new concepts and new discoveries.

Short of resetting the aging clock, there are several technologies just over the horizon that should offer substantial life extension benefit.  I believe the best prospects are senolytics (ridding the body of senescent cells), telomerase activators (rejuvenating old stem cells), and adjusting blood levels of key hormones and cytokines that increase or decrease with age.

 

The Bottom Line

Programmed aging is the right model to keep in mind as we search for interventions that slow the aging process and lessen the incidence of heart disease, cancer and Alzheimer’s all at once.  Prospects are good for real breakthroughs, perhaps as soon as 2017, but I am no longer as optimistic as I was just a few years ago that complete rejuvenation is on the horizon.

Wishing you health and vitality for the coming year,

 

 

 

– Josh Mitteldorf

From Santa Diego, a Jolla Xmas Gift

From the Salk Institute in La Jolla, CA came an announcement last week that the four factors previously identified to turn ordinary cells into stem cells (in cell cultures) was successfully used as a rejuvenation procedure in live mice.  The results provide important new evidence for the hypothesis that aging is under epigenetic control, and a proof of principle that we might slow aging by modifying the chromosome markers and attachments that determine gene expression.  But the way in which this was done involved genetic engineering before birth, and there is no obvious way to translate the results quickly into an anti-aging teatment for living humans.


Ten years ago, Shinya Yamanaka’s Kyoto University laboratory announced that just four proteins could turn an ordinary, differentiated cell back into the stem cell from whence it came.  The four were transcription factors, high level switches that turn whole systems of genes on and off with one signal, and the “Yamanaka factors” became known by their initials, OSKM.

Last week, Izpisua Delmonte’s laboratory at the Salk Institute announced a success in rejuvenating whole animals, live mice, using the same OSKM.

Whether this is the germ of a potent new rejuvenation treatment remains to be seen; but the immediate message is a dramatic affirmation of the new paradigm in anti-aging medicine: aging can be reversed by signaling, without artificially-engineered repair of damage.  A bold form of this paradigm is the epigenetic hypothesis—now just 4 years old—which says that aging is controlled by gene expression.  It is the set of genes that are turned on and off, and the genes’ levels of expression that determine the state of the body’s age.  (This idea does not deny that tissues and biomolecules suffer damage with age; but the hypothesis says that the body knew how to repair this damage at one time, and is capable of repairing the damage again, when the signal molecules engage repair mechanisms appropriately for a young individual.)

Gene expression  is controlled, in turn, by markers on the chromosome and on the histone spool around which the DNA is wrapped like thread on a spool.  These markers are known to change with age in a characteristic pattern.  Shifting epigenetic markers program all the stages of development, and (according to the hypothesis), the program continues, and causes the body to pass through the stages of aging.

But in nature this clock never goes backward.  The epigenetic clock is reset to zero as the genome is wiped clean and reprogrammed.  This happens twice: once in the creation of germ cells, the sperm and egg; and a second time after sperm and egg join to make a zygote.  (This is a simplification; some traits are epigenetically inherited, implying that some genome markers are retained and pass across generations.)

If we buy the epigenetic hypothesis, then the holy grail of anti-aging medicine would be to reset all the epigenetic markers, say from age 60 to age 20, but not all the way back to zero.  This must be “possible” in some sense of the word; but if it depends on us to read (for example) the methylation of a 20-year-old’s chromosomes and write the results onto the chromosomes of a 60-year-old, in every cell of the body, without otherwise disrupting the living organism, then the task is daunting.  And methylation is just one of about 100 known epigenetic modifications of the chromatin.

Nature knows how to reset the epigenetic clock all the way to age 0, but there is no precedent for a partial reset.  All tissue differentiation is lost, and the growth rate is pedal-to-the-metal high.  It should be no surprise that previous attempts to rejuvenate the living mouse by resetting the clock with OSKM have led to cancer disasters [ref, ref].  In this new report, the Salk researchers used short, intermittent exposure to OSKM to “partially reset” the epigenome.  If this really works, and if the epigenetic hypothesis continues to pan out, then this is indeed a week to celebrate.

 

The experiment

The procedure was first tested in human cell cultures, demonstrating “partial de-differentiation”, where functional cells were rejuvenated without returning them completely to stem cell status.  This was an important proof of concept.  The authors cite previous experiments suggesting that OSKM re-setting is a multi-step process, so it is possible in principle to halt the process after partial re-programming, and hope for a somewhat younger state.

Next, the procedure was tested on mice with genetically short life spans, living an average of  just 18 weeks.  Mice with the OSKM treatment lived 24 weeks.  Impressively, the treatment was tuned so that it did not increase cancer rates.  The particular life-shortening gene was defective LMNA (Lamin A).  Lamin A is important for structure and function in the cell nucleus (details hazy), and there is no way to distinguish from this experiment whether the OSKM treatment merely counteracts the deficiency of Lamin A or whether it slows aging generally. Finally, the procedure was tested in normal, aged mice.  They showed signs of improved healing, nerve regrowth, and mitochondrial chemistry typical of younger mice.  But the mice were sacrificed to determine these things, so there was no demonstration of increased lifespan for genetically normal mice.  Sometimes “publish or perish” pressure leads researchers to kill the goose that lays the golden egg…

But the big asterisk on this new result is that the delivery system was through a gene added to the mice at the egg stage.  It is easy to modify genes at the egg stage, when there is just one cell, and then the modification is copied in every cell of the adult; but to do gene therapy for adult humans is still at an early experimental stage.  Every cell in their bodies had an extra copy of each of the 4 genes for the OSKM factors, and these genes were so configured that they could be turned on and off with a drug (doxycycline).  Administration of the drug was arranged to be just right to reprogram the cells, but not all the way.  Optimum was found to be a low dose, just two days a week.

 

Theoretical hedging

Bench scientists have learned to adopt the epigenetic hypothesis in practice, but some are still bound to the obsolete theoretical ideas, inherited from sclerotic thinking about “selfish genes”.  Belmonte was quoted as saying the epigenome becomes “damaged” late in life “At the end of life there are many marks and it is difficult for the cell to read them.”

But studies of aging epigenomics show that in addition to random changes in the epigenetic state, there are definite, programmed changes—enough to make an accurate epigenetic clock—and that some of these changes turn down cell repair functions and turn up inflammation.  Aging involves a loss of order (“damage”), but it also entails a set of programmed changes.  It is the latter that we may hope to address through a streamlined, signaling approach to anti-aging medicine, and, if we are lucky, the body may take up the ball from here and undo part or all of the damage.

 

The bottom line

This is an important new confirmation of the epigenetic hypothesis.  Previous confirmations were

  • in parabiosis experiments, but the experiment could not be continued long enough to be sure that lifespan was extended
  • in “methylation clock” measurements, but there has been no way to distinguish whether epigenetic changes were a cause or a result of aging.

This new experiment shows that epigenetic changes can extend lifespan.  But the experiment offers no clear extrapolation to life extension for humans.  The treatment depends on four large molecules that need to be delivered to every cell nucleus in the body.  These molecules cannot be taken orally because they will not survive digestion, and even intravenous delivery will not get the molecules to cell nuclei where they are needed.

In cell cultures with the OSKM factors applied externally, stem cell yields are still just a few percent, even after ten years of experience.

The Salk researchers got around this by inserting the OSKM genes into the cell, but for already-living humans this is not a possibility.  The best we know how to do is to modify some of the body’s cells with gene therapy; CRISPR in living humans is itself a new technique in its experimental phase.

So for the foreseeable future, I see a two-pronged approach to cell-level rejuvenation.  One is to remove senescent cells (senolytics); and the other is stem cell removal, rejuvenation, multiplication in vitro, and return to the body.  OSKM may be useful in this second step, rejuvenation of stem cells in vivo.

Telomeres—too much of a good thing?

One of the major themes in aging science of the last 15 years has been that there is natural variation in telomere length, and individuals with longer telomeres have lower disease risk and longer life expectancy than those with shorter telomeres.  A paper last week in Nature Structural and Molecular Biology found that stem cell telomeres are actively maintained at a target length, not just by elongation (with telomerase or ALT) when they get too short but by active trimming when they get “too long”.  We know what “too short” means: short telomeres lead to cellular senescence.  Cells with short telomeres are not just falling down on the job; they are toxic.  But what does it mean for telomeres to be “too long”?


The headline in MedicalXpress says “Scientists find that for stem cells to be healthy, telomere length has to be just right”.  The story underneath includes the claim that “really long telomeres caused telomeric fragility, which can lead to initiation of cancer”.  But now that I’ve read the research article on which it is based and some of the references in that article, I see that the part about cancer was tacked onto a (new and interesting) research finding.  I’m convinced that the meme “long telomeres lead to cancer” has been resounding in an academic echo chamber for 25 years; that it never has had an experimental foundation, and its theoretical foundation is just wrong.

What is new and interesting is this:  researchers at Salk Institute have discovered a mechanism for trimming telomeres.  In our previous understanding, telomeres lose length every time a chromosome is copied (every time a new cell is created).  Telomeres are partially rebuilt by the enzyme telomerase, or by a less direct mechanism called ALT.  Telomeres are fully rebuilt only when new life is created, in a germ cell or a fertilized egg.  In the previous understanding, shortening of telomeres is passive, while lengthening is active.  The new study documents an active mechanism for shortening telomeres.

Part of each telomere is unpaired, a single strand of DNA extending past the end of the chromosome, and folded back over the main (double-stranded) part.  Single-stranded DNA normally means a problem, and the cell nucleus has multiple means to repair or degrade it.  To protect the telomere from being attacked (to prevent fixing of what ain’t broke) the telomere is chaperoned by various protective proteins, most famously shelterin.

We have known that stem cells can express telomerase to counteract telomere shortening, though (in humans) there is not enough to keep telomeres from shortening progressively through a lifetime.  The new finding is that when a stem cell detects that telomeres are “too long”, there is a way to trim them back.  A strand of DNA is manufactured that is complementary to the telomere’s repeated sequence TTAGGG.  The complementary strand (that would be AATCCC, repeated)  has an affinity for the telomere repeats, and it finds and binds to a segment of telomere, then circles, “bites its tail”, and breaks off a ringlet of double-stranded telomere-stuff (called a T-circle), effectively shortening the telomere.

What’s wrong with extra-long telomeres?

The obvious question: why is the cell doing this?  What is the danger of telomeres that are too long?  One natural place to look is in the telomere position effect (TPE).  Telomeres fold back over the chromosome in such a way as to silence genes near the ends.  We might expect that the right genes must be silenced at the right times, and that silencing too many genes with an extra-long telomere would cause problems.  My own best guess is that this is the right answer.

Another hypothesis is that extra-long telomeres are inherently unstable and unmanageable.  But the present studies were done with human cell cultures, where telomeres are ~10,000 BP in length; mice commonly have telomeres ten times that long without causing problems.

The conventional hypothesis is that telomeres are trimmed to prevent cancer, and that is the spin put on the findings by the authors of the paper in their press release.  “We were surprised to find that forcing cells to generate really long telomeres caused telomeric fragility, which can lead to initiation of cancer.”  In the paper itself, they were more circumspect about this explanation, as is academically appropriate.  These people are masters at what they do (Since spending time at NIBS in Beijing, I have an expanded awe for the experimental virtuosi who are able to infer reliable data about the inner workings of cells.)  But they are not theorists and they trust the community of biological theorists to supply the theoretical framework for interpreting their result.

In this case, the trust is misplaced.  The idea that telomeres are kept short to prevent cancer was originally proposed by (Nobel laureate) Carol Greider (1990), and has been promoted most explicitly by Judith Campisi (1999) before she became convinced by experimental data that the situation is more complicated, that short telomeres are more likely to cause than to prevent cancer (2013).  Through strength in numbers the cancer/telomere hypothesis has achieved “echo chamber” status–many researchers cite each other’s secondary statements on the subject, until tracing the empirical support for the hypothesis becomes unnecessary.  It is common knowledge.

One of the authorities cited in the original paper is this article which is actually about deletion of a gene for a shelterin-related protein that binds to telomeres.  When this gene is deleted, telomeres become unstable and cancer rates rise.  But the article is not about telomeres that are “too long”.  Another authority for the hypothesis that is cited in the original paper is this book chapter.  The chapter is not about cancer, but it does peripherally cite this study from NCI, which finds that cancer is associated with short telomeres, but not long telomeres.

Contrary evidence: health benefits from extra-long telomeres

Just last spring, Maria Blasco’s group at the Spanish National Cancer Research Centre gave us this study, in which stem cells with hyper-long telomeres (up to 300,000 BP) were introduced into mice (in which telomeres normally are already 10 times as long as humans’).  “Mice with hyper-long telomeres…accumulate fewer cells with short telomeres and less DNA damage with age, and express lower levels of p53….We further show that wound-healing rates in the skin are increased in chimaeric mice.”  No life span data is reported, but cancer risk was lower in the mice with hyper-long telomeres.

This study from another research group at the same institution linked the extraordinary healing and regeneration capacity of very young mice to their extra-long telomeres.

In this study from UCSF, published just this fall, heart patients whose telomeres were lengthening over the four-year span of the study had 1/3 the mortality rate of matched patients whose telomeres were shortening over the same time span.

Are short telomeres a symptom or a cause of age-related disease?

This is a controversial question only because the causal hypothesis is in direct opposition to standard evolutionary theory.  So much the worse for standard evolutionary theory.

One causal mechanism which is incontrovertible is that cells become senescent when their telomeres shorten beyond a critical length.  Senescent cells are not just non-functional, they are toxic.  Removing senescent cells from the body has been shown to lengthen life span in mice, and senolytic agents are being developed for human use.  Many of us in the life extension movement regard senolytics as the #1 most promising strategy for major life extension in the near term.

The question of causality can be answered definitively by intervening to make telomeres longer or shorter “by hand”.  If short telomeres are a mere marker of past stress, then this should make little difference in the trajectory of aging; but if short telomeres are a cause of aging, then we expect that lengthening telomeres should lengthen life expectancy and lower the (age-adjusted) risk of disease.  In fact, this experimental model has been realized several times in mouse studies, two of which are referenced just a few paragraphs above [#1, #2].  The most dramatic success was in dePinho’s Harvard lab, but there are also impressive results from Blasco’s group in Madrid.

If lengthening telomeres is an effective life extension strategy for mice, it should be all the more so for humans, who have shorter telomeres, longer life spans, and less telomerase than mice.

In the face of this evidence, there are still some influential researchers and advocates in the anti-aging community who opine that “On the whole telomere length looks a lot like a marker of aging rather than the cause of problems: the groups that primarily seek to engineer longer telomeres in search of a way to slow aging are probably putting the cart before the horse.” [quoted today at FightAging.org]  Meanwhile, Michael Fossel has initiated a clinical trial of telomerase gene therapy to treat dementia.  Cancer scares from the echo chamber are spooking the venture capital that would be so welcome for startups that are seeking to bring telomerase therapy to the public.

Can Traditional Chinese Medicine Help You Live Longer?

I have just returned from three months in Beijing as a visiting scholar at the National Institute for Biological Sciences.  My host was Meng-Qiu Dong, who heads a lab studying aging in worms.  At the end of my stay, I took a look at longevity from the perspective of Traditional Chinese Medicine.  There is no doubt that TCM has some gems to offer longevity science, but the overall effectiveness of TCM resists quantification by the usual scientific standards meaning not that it is ineffective, but that it is extraordinarily difficult to define suitable tests.  But the contrast between TCM and modern Western approaches offers us a valuable perspective on our own practices.


[Disclaimer: No one in my institute thinks much about Traditional Chinese Medicine.  They are all trained in Western scientific methodology, many with PhDs from American universities, and they tend to be more conservative, more Western than Western scientists, because they are seeking recognition from American and European bio-medical journals.  They can’t afford to have their reputations tainted by anything that might be labeled as unscientific.]

Personal note

I first became interested in China in the 1970s.  I was a Berkeley grad student, auditing Chinese I every morning at 8 before my physics classes.  I knew that I was viewing the world through lenses shaped by my own education and the culture around me; and I wondered what that world might look like from a very different perspective.

The same idea applies to Chinese medicine.  Its approach and its basis of validity, its range of effects and benefits are different from Western medical science in ways that help me question assumptions that I didn’t know I was making.  I am tempted to scour the English language literature for credible clinical trials of single ingredients isolated from traditional Chinese herbs.  I am more than “tempted” – this is all I really know how to do.  And yet I know that this is an unfair and very limited snapshot of Chinese medicine – see below.  US NIH has a page devoted to TCM, and concludes “For most conditions, there is not enough rigorous scientific evidence to know whether TCM methods work for the conditions for which they are used.”

Headliners

Berberine is derived from goldenseal=小檗碱 and is a promising anti-diabetic drug, comparing favorably to metformin, though, of course there is much less data available.  Berberine increased lifespan in one fruitfly experiment, but has not been tested in rodents.

I wrote two years ago about Ginseng (人参), the Chinese longevity tonic with the longest pedigree.  Multiple benefits have been documented, including modest effect on lifespan.

The best-documented benefits of royal jelly (蜂王浆), harvested from beehives, are for retaining insulin sensitivity.  There are credible reports of anti-inflammatory activity and promotion of wound healing.  Benefits are claimed for blood lipid profile.  There is one mouse longevity study which showed a promising 25% increase in mean LS without increase in max LS, but the control LS was suspiciously short.  Dosage was 0.05% of dry diet, equivalent to ~2 g/day for humans.

LEF’s “AMPK Activator” =Gynostemma pentaphyllum= jiaogulan= 绞股蓝 is another traditional longevity herb, found in one trial to lower blood sugar.  AMPK is a sigal molecule in the insulin metabolism.  Jiaogulan promotes AMPK, which can reasonably be expected to preserve insulin sensitivity.  To my knowledge, there have been no trials of jiaogulan for rodent life span, and just one 30-year-old study in which it was found to prolong lifespan in flies.

Huperzine-A is derived from club moss=Huperzia serrata= 石杉, and is used for cognitive enhancement and neuroprotection.

Wolfberry (Goji berry= Lycium barbarum = 宁夏枸杞 = ning xia gou qi) has been studied in connection with glycation of proteins in the skin, which contributes to skin aging.

One-liners

Acupuncture is effective for relieving pain and inflammation of arthritis [review].  Surgery patients anesthetized with acupuncture have shorter recovery times and better outcomes than patients under chemical anesthesia.  (Western science doesn’t have a clue how acupuncture works.)  Chinese herbs are effective in treating irritable bowel syndrome, and even more effective when the treatment is individualized by a TCM practitioner [ref].  Ginger in the diet is linked to lower levels of inflammation [ref]. Tree ear fungus (木耳=Aricularia) reduces risk of stroke and heart attacks from blood clots [ref], and oyster mushroom (蚝蘑) has anti-inflammatory effect and benefit for blood lipid profile [ref, ref].  Elders who practice Tai chi (slowest and gentlest of the Chinese martial arts) are less likely to fall and less likely to suffer fractures if they do fall (ref).  Meditation lowers morbidity and mortality, improves measures of mental and physical health, lengthens telomeres [my review].

Chinese and Western Medicine A general comparison

Traditional Chinese Medicine Western Biomedical Science
Legtimacy comes from thousands of years of collective experience, in oral and written traditions. Legitimacy based on statistical analysis of objectively measurable responses, averaged over large populations in the last decade or two.
Individualized treatment different for each patient. Standardized treatment; same for everyone diagnosed with a given condition.
Qualitative, multi-dimensional diagnosis. Binary diagnosis the patient has the condition or he doesn’t.
Treatment aimed at restoring long-term health. Treatment aimed at relieving acute condition.
Combination of many herbs with dietary recommendations, acupuncture, and some prescribed behaviors that seem to us random and irrelevant. One drug for one condition.
Integrated diagnosis and treatment of body and mind. Treatment of each body part or system as a separate entity.
Doctor-patient relationship is integrated into the treatment plan. Doctor-patient relationship is treated as an artifact, the “placebo effect”, noise that interferes with evaluation of the core treatment.

Those few Western scientists who pay attention to ancient medical traditions treat them as a trove of ideas for suggesting single chemicals that can be isolated and tested for efficacy, in animals and people the same way we might test any new drug.  It is hard to find funding for these tests, promising as they are, because the chemicals are not patentable.  

And when such studies are funded, they don’t do justice to the Gestalt of TCM.  If we find that individual molecules isolated from TCM herbs are potent healers, how much more benefit should we expect from synergy of the traditional combinations of herbs and the personalized diagnoses by healer with training and experience?

For all the reasons above, TCM doesn’t fit with the standard mode of scientific evaluation.  If each patient is treated differently, how can you make statistical inference?  If the doctor-patient relationship is part of the treatment plan, how can you subject the plan to a double-blind comparison?  If we test one chemical at a time, we may miss important synergies.  And if we look just at short-term outcomes, we are blind to what is most important to the patient over the course of his life.

Fictions of Western Medical Science

What can we learn about our habits of thought by immersing ourselves in another culture and looking back?  Our first reflex may be to subject TCM to standard evaluations from evidence-based medicine.  But equally important is the perspective we gain from criticizing  Western medicine fromt he vantage of TCM.  

We (Western, scientific types) know that different people’s reactions to disease and responses to treatments are highly idiosyncratic; yet we treat all differences as though they were random scatter in the data, and look for one-size-fits-all treatments.

We know that drugs interact with one another, including both synergies antagonisms, and that these .   All of life depends on homeostatic balance among thousands of active chemical agents, catalytic enzymes, and signal molecules.  Yet our research is based on testing one drug at a time. Building knowledge from the ground up is the only way we know how to do science.   Less than one experiment in 100 looks for pair-wise interactions, and almost none explore the effects of a dozen or more treatments in combination.  

We value predictability and reproducibility, sometimes to the neglect of miraculous effectiveness.  We imagine that the world is a predictable clockwork, of which our task is to learn the mechanism, and we are suspicious of any intervention that works only some of the time.  We disdain anecdotal evidence.  Thousands of credible stories of one-off cancer cures are discarded in the dustbin of quackery; we refuse to learn from them because other people given the same treatment were not cured.

We have moved toward standardization of medical practice.  American caselaw in medical malpractice sets a disastrous incentive structure, defining malpractice as doing anything different from what the majority of other doctors are doing.  A good doctor’s experience and subjective intuitions can potentially provide a treasurechest of treatment options, but in America there is a powerful legal and cultural discouragement from trying anything that is not “the standard of care”.

As medical knowledge has multiplied, Western medicine has moved toward specialization.  We rely on experts who know one field, even a single disease, or even a single treatment for a single disease in great depth.  With specialization, we have lost the generalist’s knowledge of interacting body systems and organs, and the art of gathering diverse symptoms and observations to infer a diagnosis has been replaced with algorithmic medicine.

Background Western and Eastern Thought

Western science doesn’t have life completely figured out yet this is no surprise.  “Too complex” is the common refrain, but I think the problem may be deeper.  Since the 19th Century, biology has been committed to a reductionist approach.  Modern biologists are committed to a program of building an understanding of life from the bottom up, beginning with molecules.

It’s commonplace to say that Eastern thought is more holistic, Western more reductionist.  Many of the principles of Chinese medicine are conceived in terms that make a Western scientist snicker, and many are tempted to dismiss the whole field based on its theory.  But the other side of Chinese medicine is that it incorporates thousands of years of experience, and the treatments that have survived the centuries are the ones that work.  For example, the whole field of acupuncture was once dismissed as superstition, but now is accepted as a set of techniques that work for pain relief and sometimes for healing, but Western medicine has no way to think about its mechanism.

There are MDs here who practice both TCM and Western medicine, and they have the experience and the wisdom to know which patients will respond best to one or the other approach.  There are drug stores here that carry Traditional Chinese Medicine alongside their prescription drugs, in a separate department.  

A typical Chinese prescription consists of a bag full of a dozen or so herbs and roots that are boiled, and the broth imbibed once or more per day.  It’s safe to assume that tradition has combined these herbs in these combinations for a reason, but the Western analytic approach is yet quite far from a predictive science of how they interact.  The moral is that when we encounter evidence for the effectiveness of TCM, we should resist the temptation to look for the Active Ingredient, lest we risk killing the goose that lays the golden egg.  

I would like to see a study of people who have used TCM over several decades, not just to treat a particular malady but as a tonic for general health.  Compare specific health outcomes as well as morbidity and mortality for a cohort of such people with a matched cohort that has comparable diet, income and lifestyle, but does not use TCM.

Optimizing the Placebo Effect

Don’t look down on what Western medicine calls the placebo effect.  While its power is universally acknowledged, Western institutions do nothing to try to get the most out of the doctor/patient relationship, and in fact the Balkanization of medicine and the economic pressures that have progressively curtailed doctor/patient interactions speak loudly of disdain for the power of “bedside manner” in the healing process.  The mind/body connection may not be understood, but it is of paramount import, probably as powerful as all of Western medicine combined.  It is only common sense that some practitioners will be much more effective than others, and that time to foster a human relationship has potential both to restore meaning and satisfaction to the work-life of physicians, and also to turn them into more effective healers.  In contrast to Western medicine, a personal connection with the doctor is well-integrated into the culture of TCM.

Random observations on Chinese health and longevity

China is westernizing at a pace and TCM is declining in popularity, especially with the younger generation.  At the same time, TCM and acupuncture in particular are gaining adherents and practictioners in the US and Europe.

Life expectancy in China is 75 years, compared to 79 years in Taiwan (tied with USA), 85 years in Japan.  The amount that Americans spend per capita on health care is about $9,000, compared to $1,800 in Taiwan and $500 in China.  In fact, Chinese expenditure on everything put together (per capita GDP) is only $8,000.

Two thirds of Chinese men smoke (compared to <20% in the USA), but the smoking rate for women is actually lower than the US.  Only recently, the Chinese government has begun measures to reduce smoking, beginning with a ban in public buildings in 2010.

I have seen people in China eat liberal quantities of rice with each meal, and yet the obesity rate among Chinese men is 0.6% compared to >30% in America.  The weight difference is something you might readily notice while walking around any Chinese city.  The traditional Chinese diet includes small bites of meat as a condiment, but with recent prosperity has come increasing meat consumption.  The “sweet tooth” as an addictive affliction is less prevalent in China than the West.  “Gym rats” can be found in China, but much more rarely than in the US.  People have more exercise built into their day, less time set aside for exercise as a Thing To Do.  Chinese cities have undergone explosive growth in recent decades.  Pollution in Chinese cities (Beijing is worst) is bad enough to be a major factor in mortality statistics.  

…and a glimpse of the modern side of Chinese medicine

This week, oncologists at Sichuan University Hospital in Chengdu announced that they had used CRISPR technology for the first time in a human medical application.  Immune cells were harvested from a lung cancer patient, and the cells were treated with CRISPR-Cas9 to remove the gene for a protein called PD-1.  The function of PD-1 is to help killer T-cells identify the body’s own healthy cells and make sure that the immune system does not attack them; but some cancers have learned to evade immune attack by displaying a PD-1 target.  The Sichuan team cultured the modified T-cells and returned them to the patient, on the theory that they might renew the body’s failed immune response to the cancer.  Results of the trial are not yet reported.  Principal Investigator Lu You emphasized that this is a small trial focused on safety, and ten patients will be closely monitored to look for indications that the modified immune cells have attacked the patient himself.

The Bottom Line

The Western, scientific approach to medicine is my paradigm and (I presume) yours; but it is not the perfect paradigm or the only paradigm.  People who dismiss the 2500-year-old wisdom of TCM as superstitious nonsense are missing a potential influx of new ideas and an opportunity for self-reflection.  It is only by getting outside our paradigm that we can see its limitations, realize that our thinking has been within a box.  

Research scientists in America and Europe have to compete for grants and have to get their work accepted into one or another elite journal.  This creates incentives to stick to the kinds of biological questions that can be addressed through standard methodology, that will yield definitive answers within a few years at a cost the lab can afford.  We can hardly expect  researchers to behave otherwise.  But we might, at least, recognize that the system steers researchers to ignore approaches that involve multiple coordinated interventions, that rely on experience or expert judgment to be tailored to individuals, or that work via pathways that we do not understand.  We ought to recognize that some promising treatments for life extension and health have been excluded from investigation “in the name of Science”.

In an Age of Epigenetics, Does Antagonistic Pleiotropy Still Make Sense?

The dominant theory of aging today was conceived at a time when genes were thought to be biological destiny.  Handiwork of George Williams, it is called Antagonistic Pleiotropy.  Pleiotropy is the idea that one gene can have multiple effects, and the core of the AP theory is that there are genes that give us strength and fertility in youth, but they cause havoc later in life, ultimately destroying the body.  Fifty years after Williams, we now know that genes are routinely turned on when and where they are needed, and turned off most of the time.  More than 97% of our genome is devoted not to genes but to epigenetics, which is the regulation of gene expression, and a mainstay of 21st century molecular biology.  Why should the body ever be stuck with a gene that is doing it harm?   Can antagonistic pleiotropy be re-cast to make sense in this age of epigenetics?  


In 1957, George Williams proposed an evolutionary theory of aging that later became known as Antagonistic Pleiotropy, and under than name has been the most influential theory of aging to this day.  It has formed the basis for interpreting a huge variety of phenomena in aging labs around the world.  Pleiotropy is routinely invoked to explain results in genetics, and “evolutionary medicine” is guiding (or misguiding) research priorities for the future of anti-aging science.

Williams began with the idea (still dominant today) that rapid and copious reproductive output is the ticket for evolutionary success.  A mathematical measure of time-weighted reproduction is the Malthusian Parameter r, which Williams assumed (many today agree) is as good a mathematical translation as we have for Darwin’s concept of “fitness”.

I have argued that there is more to fitness than reproducing as fast as possible. The very word “fit” came from the notion of traits appropriate to a particular environment, a particular ecosystem.  Ecological consequences can’t be separated from individual fitness.  Any individual that achieves a growth rate (r) that is higher than species further down the food chain has only a very short-term fitness advantage, because its grandchildren risk starvation.  I’ve written about fitness in an ecological context here and in my new book.

Genes “your way”!  Tucked away when you don’t need ’em

Today, I am offering another reason to discredit antagonistic pleiotropy.  Williams’s theory is rooted in the idea that if a gene is selected in evolution for its advantage early in life, then the bearer of that gene is stuck with it late in life as well.  Now that we know how routinely genes are turned on and off in particular tissues, at particular times, for just a few minutes or for years on end, it is no longer credible to imagine that the individual is stuck with a gene at a time when it has become a liability.  Can we find a way to make sense of antagonistic pleiotropy in the context of complex and robust epigenetic adaptation?

I’ll say this much for pleiotropy: some of the genes most detrimental to the body do indeed have “legitimate” functions (good for the individual or her reproduction).  I have come to see the proximate cause of aging as a re-balancing of hormones, some turned up and some turned down, with detrimental effect.  Inflammation is turned up too high.  Apoptosis is turned up generally, causing loss of perfectly good muscle and nerve cells, but the strong apoptosis signals that kill cancer cells before they can become tumors becomes less effective with age.  Melatonin (for the circadian clock) and glutathione (antioxidant) and CoQ10 (cellular energy) are all in progressively shorter supply as we age.

It is common to call this rebalancing “dysregulation” and ask what went wrong [example, another, a third].  But I don’t think evolution makes such big mistakes.  I see not dysregulation but  re-regulation or even re-purposing of a system that protects the body, toward the end of self-destruction.

Mikhail Blagosklonny has written often about a theory in which aging comes from the body’s inability to turn off the genetic program that led to development and growth early in life.  He knows his stuff, and writes convincingly about particular genes (notably mTOR) and the evidence that they are being kept on later in life, when their main consequence is to increase inflammation, promote disease and shorten lifespan.  I question only the part of Blagosklonny’s theory that says this is an accident.  I see it as one of the many instances in which genetic machinery is repurposed.  How does Blagosklonny explain this mistake?  “A potential switch that would turn off the developmental program cannot be selected, because most animals die from accidental death before they have a chance to die from senescence. A program for development cannot be switched off, simply because there is no selective pressure against aging.”  This idea has a venerable past, but no future.  Indeed, there is selective pressure against aging, and the cost of aging in the wild can be as high as 70% of fitness, though it is typically about 20-30% [ref].  This idea that aging comes about because no animals in the wild live long enough to die of old age was a brilliant insight due to a Nobel immunologist sixty years ago; but today it is no longer tenable.

Oft-cited Example of Antagonistic Pleiotropy

A classic example used to illustrate pleiotropy is Huntington’s Disease.  This is a congenital syndrome caused by a gene variant that actually increases fertility early in life, but typically around age 40, neurological symptoms begin, affecting coordination and causing mood swings.   Brain cells die, and Huntington’s is eventually fatal.  Huntington’s is not normal aging, of course, but the idea is that there are other genetic variants that are so common we don’t think of them as diseases but they are also promoting fertility early in life and degeneration later on.

In this case, it is not the timing of the gene but the version of the gene (allele) that is caused.  Is Huntington’s Disease truly an example of antagonistic pleiotropy?  Yes, in the sense that the allele causing Huntington’s Disease has both a benefit and a cost, and the cost is connected to disease and death later in life.  But no, in the sense that natural selection has actually rejected the Huntington’s gene time and again.  The Huntington’s mutation is one that occurs spontaneously in one child, and then is transmitted to children and grandchildren.  It lasts for several generations, but would disappear from the population were it not for the fact that it is constantly being re-introduced by fresh mutations.  Here is an allele with early benefits and late costs that is being rejected by natural selection on an ongoing basis.  So should Huntington’s be considered a counter-example to the AP theory?

Grade inflation for (some) scientific theories

Nowhere in science are theories given a pass when contradicted so frequently and so flagrantly as in evolutionary theory of the selfish gene.  Manuscripts describing evidence against the selfish gene, or theories based on group selection are routinely rejected for publication.  (This situation isn’t nearly as bad as it was 15 years ago.)  But Antagonistic Pleiotropy continues to get by with a “gentleman’s C”, because (like the Ivy League preppies), the theory has a pedigree.

“Direct experimental evidence for age-specific effects of mutations comes from only a handful of reports” [Scott Pletcher and Jim Curtsinger]  These geneticists actually mutated fruitflies at random and went looking for gene variations that could cause benefits at one stage of life and costs at another.  And they found them!  Except, curiously, they were all at early stages of life, and none affecting old age [ref].  “The main evolutionaty models of senescence are antagonistic pleiotropy and mutation accumulation, neither of which has substantial experimental support.” [1995]  Yes, that was written move than 20 years ago.  The difference today is that we now have a huge body of evidence contradicting each of these theories.

May we live to see the day when scientists look back at the theory of Antagonistic Pleiotropy, scratch their heads and say, “I wonder why people would have believed that!”

AgingAdvice page is back online

Thanks to some of my readers who noticed that AgingAdvice.org had disappeared.  It is now back online.  FMDRecipes.org is also back online.

(The site had been hosted by GoogleDrive, and I missed Google’s announcement that they would no longer be supporting public web pages.  The page now has a permanent home at Site5.com.  The web address remains the same.)

Putting the “system” back in Systems Biology

Cold Spring Harbor labs on Long Island has a diverse offering of conferences that attract experts from all areas of biology. For the last six years, there has been a sister group organizing conferences in Suzhou, China. I spent last week at the 2016 CSH Asia conference on Systems Biology.

While I have been to many conferences on aging and a few on evolution, this was my first Systems Biology conference. I looked forward to learning how biologists think about whole-body issues of homeostasis, organization, and (maybe if I was lucky) blood signals that regulate aging.

What I found instead was that researchers in systems biology are doing what other biologists are doing: they are babes in toyland, exploring the potential of a seductive array of new biomolecular tools. They are compiling catalogs and making maps and correlating every chemical they can find with every other chemical, and collaborating with statisticians to look for patterns in the data. If “systems thinking” is from the top down, what I found at this meeting was just the opposite.

A hundred years ago, Lord Rutherford said that “All science is either physics or stamp collecting.” He was mocking the biologists’ program of collecting specimens, classifying and cataloging them. Twentieth century biology turned this around; it was neither physics nor stamp collecting, but model-building. Systems biologists in particular have analyzed living organisms in terms of signals and networks and energy flows, and have generated a great deal of understanding. At its best, biology has forged a new mode of science.

So why is it that 21st Century systems biology is looking once more like stamp collecting? It’s a question I asked one of the conference organizers (in more polite terms), and he responded that “we are working from a reductionist framework. We are trying to build understanding from the bottom up.”

There’s a deeper answer

Why, after the revolutionary successes of late 20th century biology, should bioscience find itself back at square one, trying to build a foundation? The short answer: genetics is simple; epigenetics is complicated.

The heyday of genetics started from Crick’s decoding of the genetic code in 1961. DNA was revealed to be a blueprint for producing proteins that would do the body’s work. The code was just as simple and elegant as it could be, and the machinery to do the translation was segregated in ribosomes, which could be isolated and picked apart. The era of genetics ended in 2003 with the completion of the human genome project. Results were a surprise to everyone, and the message took awhile to filter into conceptual thinking: The genome is 3% genes and 97% gene regulation. All the impressive tasks of development, homeostasis, and metabolism are performed by an exquisitely adapted system that turns genes on and off in the right place at the right time.

2003 ended the era of genetics and began the era of epigenetics. How is gene expression regulated and contolled? DNA methylation was the first mechanism discovered. But as clues appeared and mechanisms were partially elucidated, it has become apparent that epigenetics is as complicated and intractable as it can possibly be. Besides methylation, there are more than 100 modifications of the DNA and its associated proteins (histones) that affect gene expression. There is also the way in which DNA folds around itself, leaving some regions open where they can be transcribed and keeping other regions under tight wraps. Finally, there is a variety of post-translational modifications; even after a stretch of DNA has been transcribed into RNA and translated into a protein, the protein can be turned on or off by adding a phosphate group or a methyl or acetate at any number of receptor sites.

Metabolism is now seen as a dense web of interacting processes, intertwined causes and effects. Gene network maps draw lines between genes that are co-expressed, and can divide the territory into subsets (modules) that are more closely related to each other than to other modules.

 

But this is a picture that only a computer could love; it contains intricacies on a scale that human consciousness cannot grasp with conceptual understanding.

Contrast this to the naive simplicity of Crick’s Central Dogma of Molecular Biology: Information flows in one direction, from DNA to RNA to proteins. Crick lived to see his insight de-dogmatized by exceptions, but it has been since his death (2004) that the essential, bewildering complexity of biochemical networks has been revealed.

No wonder the community of systems biologists feels that they are starting over again, collecting, classifying and cataloging stamps.

New Tools

Biochemical science this last few years seems to be driven by newly available technologies. These are so powerful and coming so fast that just exploring what they can tell us is occupying the lion’s share of available funding and lab space. I knew about some of these, and several more were new to me last week.

  • CRISPR-Cas9. This is a tool adapted from bacterial defenses against viruses. It has made it easy to delete a particular gene within a living cell culture, and perhaps within a living, breathing animal. It has been adapted to insert an exogenous gene at a particular location on a particular chromosome, and even to modify a particular section of DNA to turn a gene on or off. Cas9 has been limited to small “payloads”, adding short sequences of DNA, but just last year, techniques were reported for splitting a larger payload among multiple Cas9 vectors [Ref1, Ref2] in such a way that they piggyback.
  • Hi-C is a modern, computer-intensive version of a 20-year-old procedure for mapping a coiled and folded chromosome in 3-space. First, the chromosome is frozen by introducing random bonds between nearby strands. Then it is fragmented with a DNA slicing enzyme. Then the pieces are sequenced (this is the new part) with high throughput sequencing that can tell you which genes are physically closer to which other genes in the folded, 3-D configuration.  Finally, the computer can be used to reconstruct a picture of the 3-D configuration.
  • ATAC-Seq. This is a tool for finding the genes that, at any given time, are in open stretches of DNA (euchromatin), available to be transcribed. Chromosomes are peppered with an enzyme that slices up DNA. The fragments are then collected and sequenced, and a computer program matches the fragments to map where they came from. The DNA that was tightly-packed (heterochromatin) contributes few fragments because the enzyme can’t reach it. Thus the genes that are seen are representative of what is available for transcription.
  • Methylation mapping. Methylation of C’s in stretches of C-G-C-G-C-G-C-G-C-G within a chromosome is the best-studied mechanism of epigenetic regulation. Just in the last few years, it is possible to map the methylation state of an entire genome. A chemical transformation transforms only unmethylated C’s to uracil in a strand of DNA (with bisulfite), leaving the methylated C’s unconverted. By sequencing the strand before and after this transformation, and using a computer to map the differences, the places where C’s were methylated can be identified.
  • ChIP-Seq. If you know of a particular transcription factor—a protein that binds to DNA and turns certain genes on or off—then this technique can tell you where on the DNA the protein attaches itself. The technique combines two older technologies: immunoprecipitation, where an antibody is introduced that picks out one particular protein, and high-throughput sequencing, which identifies and locates the patch of DNA that is stuck to the CHIPped protein.

Gene expression maps have been around for a few years. They provide an enormous amount of information about what genes are being expressed where and when, but they are notoriously difficult to make sense of.  More recent are correlation maps, in which every gene is correlated with every other gene in a huge matrix that shows how likely they are to be expressed at the same time. I am intrigued by principal component analysis. You can start with a set of genes and measure all the cross correlations, and the math comes up with a combination of the genes most likely to be expressed together (Principal Component #1).

Sometimes a single gene sticks out, and the authors conclude that this particular cancer can be treated by targeting this particular gene.

More often, the results show a combination of hundreds of genes that tend to be expressed together in a particular proportion, say 1.2% gene #1, 0.04% gene #2, 0.15% gene #3…and so on, with coefficients for hundreds of genes. This is the output of a principal component analysis. If such a profile is identified with a healthy state, or a young state, we do not yet have the capability to shape this profile of gene expression in a cell culture, let alone in a living animal. But it is not inconceivable that we will acquire this ability with advancing biotechnology of the coming decade(s).

 

The Harvard laboratory of Brenda Andrews is fully automated, with robotic handling of yeast culture plates, robotic data collection, computerized data analysis. All that’s left for the human to do is to write the historical introduction and submit the manuscript. I am a fan of artificial intelligence and computer learning for some applications. Computers have their own ideas of what constitutes a pattern or a trend. They often come up with unexpected solutions to problems, even simple solutions on rare occasions. But AI never produces elegant theories or new ways to look at the big picture. We give that up when we rely on computers to do science for us.

Growth, Development and Aging

Growth and development are programmed, to be sure, but (so far as we know at present) there appears to be no central coordinator of the process. Rather, the tangled web of chemical signals adapts and responds to changes in the body and in itself. The intelligence is not in a central brain, but is distributed through the system itself. There is no one calling the shots. The metabolism behaves intelligently the way a beehive behaves intelligently, though no single bee has a a clue concerning the hive’s plans and strategies.

I have bet my career on the thesis that aging is a metabolic program, a continuation of the process of development into a phase of self-destruction. I used to think that this meant there were genes for aging. I was the most optimistic speaker at the anti-aging meetings. “All we have to do is find the aging genes and turn them off.”

Then I accepted the new picture centered on epigenetics. I thought that chemical signals were arranged in hierarchies, with a few hox genes and transcription factors controlling a much larger number of workhorse proteins that actually get the job done. The job of the anti-aging scientist is to re-balance the transcription factors to create a more youthful profile, and the workhorse proteins would dutifully take care of the rest.

But more recently, I learned that there are thousands of transcription factors, comparable to the number of genes they regulate.  And the lines between promoters, enhancers, transcription factors, and metabolites has been blurred.  A less optimistic scenario is beginning to come into focus for me. I believe that aging is a continuation of the developmental program, but development is inscrutably complex, and it seems to be controlled by a web of interacting molecules that play multiple roles. Each one is a cause and an effect. Many have roles both a regulatory agents and also as workhorses. There’s no one in charge of the factory. The factory is designed so ingeniously that it runs itself.

Study of Development may be a Key to Aging

Much is known about details of development, but there is no systemic understanding of how the process is put together

    • How much is predetermined in cell lineage?
    • How much is self-organization?
    • How much is centrally organized, through internal secretions?
    • How do these three interact?

Of course, the same questions may be asked about aging. It may be more feasible to approach these questions through development than through aging, (1) because development happens on a faster time scale, (2) because aging contains a stochastic element not present in development, and (3) because the phenotypes of development can be observed clearly and locally. I recognize that this suggestion means going back to basic science to make a long-term investment in understanding of aging, but maybe that’s what we need.