A genomic predictor of lifespan in vertebrates | Hacker News Reader

A genomic predictor of lifespan in vertebrates

nature.com

117 pointsVaslo77 comments

> In the past 200 years, the average life expectancy of humans has more than doubled because of modern medicine and changes in lifestyle

I thought this idea that humans had short lifespans historically was thoroughly debunked. Humans have historically had high infant mortality rates which threw the numbers off, but if you survived past the age of three you were pretty likely to make it to your sixties or seventies.

Your second sentence directly contradicts your first.

Maybe a better way of putting it is that averages are a garbage statistic when looking at these numbers, because they hide the fact that the normal human lifespan is and always has been roughly the same.

Mortality rate actually reaches its minimum around age 10 or 11, so you would see even longer lifespans if you only look at people who survive at least to their teens.

> Our days may come to seventy years, or eighty, if our strength endures; yet the best of them are but trouble and sorrow, for they quickly pass, and we fly away.

How old is this proverb?

youngest is within a 500 year window around the date of the composition of the Psalms (it's psalm 90)

https://en.wikipedia.org/wiki/Psalms#Origins

It's true that infant mortality has decreased faster than other mortality in the past century. Even people who survived past infancy had significantly higher mortality rates at the beginning of the 20th century, though.

See "Table 6 - Period Life Tables for the Social Security Area by Calendar Year and Sex" for detailed information from the United States:

https://www.ssa.gov/oact/NOTES/pdf_studies/study120.pdf

In the table series for 1900, male life expectancy at birth was 46.4 years and female life expectancy was 49 years. For the survivors of infant mortality, additional life expectancy at age 6 was 53.2 years and 54.3 years respectively. Most children could not expect to reach their 60th birthday even if they had survived infancy.

At age 18, remaining life expectancy was 41.7 and 42.9 years, for total expected age at death of 59.7 and 60.9 years respectively; weighted by sex distribution at age 18, these young adults had an average life expectancy of 60.3 years.

I don't think that looking at lifespans for the industrial revolution has any bearing on what lifespans used to be 'historically'. It was pretty clear to me, from reading the GP that they were talking about pre-industrial revolution times.

Remaining life expectancy at age 18 was even lower in 1800 or 1700, from what I can tell. You can find small exceptions (like aristocrats in particular countries) but I'm not aware of any large (50,000 people or more) preindustrial population where the average teenager could expect to die older than age 60. I would be delighted to see counterexamples.

EDIT: This was interesting.

"Lifespans of the European Elite, 800–1800". It examines the lifespans of European aristocrats over the thousand years prior to the Industrial Revolution. It limits its analysis to people who reached at least 20 years of age. Per Figure 8, the average lifespan remained below 60 in the entire time period.

https://www.cambridge.org/core/journals/journal-of-economic-...

I wonder what pre-agricultural lifespans were like? I read recently that humans were significantly taller and healthier before agriculture, due to getting nutrition from many sources rather than a few crops. I expect they were much lower than in the cities, despite the nutritional advantage.

> pre-agricultural lifespans

Probably short. Putting aside predation, disease and starvation, there is evidence (see Pinker) that violent death was a common way to go in nomadic tribes.

Violent death was common, sure, but not necessarily more so in pre-agricultural times. See e.g. the early chapters of "Sapiens" (Yuval Harari). Agricultural revolution led to lower standard of living, increased risk of starvation (feast-or-famine dependence on fragile harvest), increased health issues (less-varied diet, also disease rampant in denser populations), and whereas in the presence of potentially hostile competition nomadic hunter-gatherers could choose to move, farmers would logically choose to stay and fight rather than leave the farm and almost certainly die. The agricultural revolution was a pretty bad deal for most people for most of the time since it began.

The farmers won. Why would they choose to farm if there were no advantages?

What happened was that farming was so successful that the human population boomed. When famine did occur, it caused more deaths because there were more humans.

Farming societies are more hierarchical and have more people. For the ones in charge that is for sure advantageous.

Also it’s a bit of a trap: as soon as you switch over you cannot go back, as foraging cannot sustain as many people. You will have to constantly expand to feed the growing population.

> whereas in the presence of potentially hostile competition nomadic hunter-gatherers could choose to move, farmers would logically choose to stay and fight rather than leave the farm and almost certainly die

You might think this, but the historical pattern -- everywhere -- is that farmers stay where they are and get conquered by more mobile non-farmers. They don't so much fight as submit.

> See e.g. the early chapters of "Sapiens" (Yuval Harari).

This part of Harari's book have been debunked quite a few times already: his views of pre-agricultural are romanticized and doesn't match with the work of the specialists of this period. (While Harari is indeed an historian, he's a specialist of medieval times and has little authority on early-humans history).

Btw, I'm not even disagreing with you about agriculture, I just wanted to point out that quoting Harari on that has really little value.

Thanks, @littlestymar. To me, Harari's take seems more neutral than "romanticized". I share his skepticism of those who claim concrete knowledge of aspects of pre-literate human culture at which, logically, one can only guess or imagine. This might counter your point about his relative expertise / authority for that time period.

That said, I'm no historian, just a layperson who found Harari's work (so far -- I haven't yet finished "Sapiens") thought-provoking and interesting. In the relevant early chapters his perspective is refreshingly different from the norm -- in some ways comparable (for me) to Zinn's "A People's History of the US", in that it provides a PoV sufficiently removed from the standard narrative to serve as a reminder of how shallow and incomplete any one-sided version of events must be. The GP's citing of Pinker likely belongs in this camp, too: referencing an author whose ideas have merit (eg Pinker's computational theory in "How the Mind Works"), independent of their ultimate status as authoritative works.

Hunter gatherer cultures don't have as many issues with disease spread because of the low population density. If your little community has a couple dozen people, even a 100% morality rate doesn't tend to spread past the couple dozen. Plagues really require high density agricultural societies.

This isn't true. Most studies of virgin soil epidemics have been in modern foragers and all of the "common" agents I could think of in a minute (Y. pestis, tuberculosis, smallpox, malaria...) evolved long before agriculture was invented.

http://sphweb.bumc.bu.edu/otlt/MPH-Modules/EP/EP713_History/...

>Since they lived in small groups and moved frequently, they had few problems with accumulating waste or contaminated water or food.

>The shift from the hunter-gather mode of living to an agricultural model provided a more secure supply of food and enabled expansion of the population. However, domesticated animals provided not only food and labor; they also carried diseases that could be transmitted to humans. People also began to rely heavily on one or two crops, so their diets were often lacking in protein, minerals, and vitamins

>Rodents and insect vectors were attracted to human settlements, providing a means of spreading disease.

That page is intended for a lay audience. I'm not sure a single sentence of the first paragraph is correct. Everything from the dates to the statements about mobility and nutrition are questionable or plainly incorrect.

Instead, here's Lifeways of Hunter-Gatherers. From the 2nd ed., p. 200 on disease:

> An important cause of childhood death in many forager societies are infectious and parasitic diseases, including respiratory tuberculosis (TB), influenza, pneumonia, bronchitis, and diarrheal diseases resulting in dehydration.

> Among the Dobe Ju/’hoansi, disease, especially TB and malaria, account for 85 percent of childhood deaths ... and violence for 8 percent.

> Infectious disease (with most deaths occurring among infants and juveniles) accounts for 85–95 percent of Agta deaths

One weakness of current literature is that the mechanism by which adults get sick (contact with other adults) is radically different for living foragers than our paleolithic ancestors. With that said, the fact that we still have these epidemic diseases with us today demonstrates that they were able to survive in ancient populations (excepting plague, which is resident in marmots and only "accidentally" infectious to humans). Perhaps larger regional group sizes and a functioning long-distance forager trade network helped these diseases to survive where they struggle today, but survive they clearly did.

The work of Pinker you refer to has been thoroughly debunked as pseudoscience -- the concrete point about nomadic tribes may or may not stand, regardless, of course.

I’ve heard lots of substantive criticism of Enlightenment Now, but less of The Better Angels of Our Nature. Do you have sources to rebut the latter? I read Better Angels, and some associated reviews, and most of the critical reviews seemed to stipulate all the facts in the book and were left to express sour grapes, or a hang-up with the perceived idea of de Chardin-esque progress (which I don’t think Pinker was advocating; he was clear he believed in the factors, and that those factors were not inevitable or inexorable).

There was a long back and forth between Pinker and NN Taleb. To me it seemed that Pinker didn't properly address any of Taleb's concrete critical points.

Problem with that is that pre-agriculture you cannot sustain a large number of people, so it is very doubtful that the population could sustain themselves better than with agriculture.

Why would a super healthy pre-agricultural society move to agriculture if it was doing worse than before.

Because for individuals making rational decisions, tending to crops and livestock is easier than hunting and gathering, and it won't necessarily be obvious over the timescale of a lifeapan that such a lifestyle is detrimental to health, especially if you're talking about a pre-scientific, pre-literate society with no real form of record keeping.

Plus, the shift is going to be gradual - you start by supplementing with a small garden, a handful of captive prey animals during hard times, then after some number of generations you come to rely more and more on agriculture without necessarily realizing why or even if your tribe is showing minor signs of mysterious illness. And then if you do realize that something is up, you're probably cursing the earth/gods/demons for your illnesses, rather than coming to understand the true variety required in a healthy diet and abandoning the convenience of your farming practices, which are in no way an obvious problem.

Tending crops is not easier than hunting. Especially in the early Neolithic when bronze hasn't even been discovered yet. But even today, farming is tougher than hunting. The difference is that farming and animal husbandry scales tremendously well. Predators regularly die off in the prey-predator cycle. Agriculture when done right and under favorable climates is predictable and scalable.

Pick between spearing a bison or gazelle with a rock tip, or harvesting from a small plot of not quite domesticated, hardy crop that you just scattered somewhere fertile, and putting off the hunt for a few more days. Or a proto-goat you keep tied up somewhere where it can graze.

It's a gradual process and has immediate benefits even on a small scale with relatively low investment. Consider also that women were probably not hunting, and probably had some spare time when they weren't gathering/taking care of kids or what have you. It's pretty easy for a community of Hunter gatherers to have occasional free time, if you look at data from more recent tribes from the last hundred years or so. Plus there's all kinds of art and such...simple crop rearing and basic animal raising isn't hard to imagine.

A Bison will feed a whole tribe for a month. You can only harvest most crops once a year. Veggies don't bloom all the time. By 10K years ago, humans had already invented the bow and arrow. They also had other clever techniques. Definitely worth the risk. The modern crops we eat today didn't even exist in the wild. It took thousands of years of selective breeding to get modern vegetables and tubers. Throwing seeds is NOT enough to grow real crops in any amount that will actually feed anyone, especially the kind of crops that were around 10K years ago. Farming takes a fuck ton of work. You have to water them, you have to fertilize them, you have to defend them from other animals, you have to weed out other plants competing with it for resources. It's not a simple thing. It's back breaking labor. There's a reason why 90+% of the population were farmers until the invention of gas engines, automated harvesters, electricity, etc.

>Throwing seeds is NOT enough to grow real crops in any amount that will actually feed anyone, especially the kind of crops that were around 10K years ago.

Yes, that was one of my points. The initially farmed plants were fully wild and hardy enough that they probably could be grown just by scattering seeds around.

>Farming takes a fuck ton of work. You have to water them, you have to fertilize them, you have to defend them from other animals, you have to weed out other plants competing with it for resources. It's not a simple thing. It's back breaking labor. There's a reason why 90+% of the population were farmers until the invention of gas engines, automated harvesters, electricity, etc.

Again, we're not talking modern, large scale optimized farming of GMO crops that would not survive without human care. We're talking about small, gradually expanding plots of almost wild, and therefore low maintenance, supplemental crops, that over generations become a larger and larger part of diet. How else do you think farming started?

A bison will feed a whole tribe for a month, sure, but it can also take tribe members with it, especially with your stone tipped, non compound bows. If you happen across an unusually supportive yield of whatever semi wild tubers you planted and basically forgot about, there's no reason a human wouldn't put off a dangerous hunt.

Anyway, the original question was why Hunter gatherers started farming if it were bad for them. I'm trying to show how it's possible for that to have happened. I'm not sure what you're arguing, that farming could not have occurred in any beneficial capacity before combines? Have you ever had a vegetable garden? Hardly backbreaking work if you're lucky enough to have good soil and the right climate for whatever you're growing...

Again, this is a gradual process. Hell, I can think of a modern analogue that I've picked myself, the blue Camas plant that grows all over the PNW in patches. It doesn't take much work once you've figured out you can plant them yourself next to your cave/camp.

Well I agree with you on the point of crops starting as supplements and then gradually becoming a more significant part of the diet and especially after the climate shifted from the last glacial period to the early Holocene warmth.

Even just 3-6 adult human men with spears is a force to be reckoned with in the animal kingdom. They're capable of strategizing, trapping, corralling, etc. Also, animals weren't just used for food in the stone age, the bones were used for structures, tools, etc. The leather was used for clothing, warmth, huts, etc. Humans certainly continued to hunt in the early days of agriculture.

It probably was the case that other humans less capable of hunting due to higher risk and lower strength (elderly, women, children, injured, etc) gathered and tended crops to contribute to the tribe.

Like you say, agriculture gradually got more and more efficient. Better tools, better breeding, etc, and the tribes that grew crops and raised animals were able to feed more people than the ones that hunted and gathered alone. This intensified after the bronze age.

Agriculture is beneficial because it causes abundance and predictability, even if it is more work on average. It's a ton of work to produce even 430,000 kCal of veggies (the amount found in a single modern cow), especially with early breeds of potatoes (which were tiny). I would wager that if you did the energy spent vs energy acquired calculation that hunting comes out way ahead of farming.

With farming you have to plan ahead for months at a time. The difference is that agriculture manifests abundant energy for consumption that would otherwise not exist. That's a huge evolutionary advantage, and obviously the entire reason we're able to have this discussion hundreds of miles apart from each other at instantaneous speed.

Can’t we derive some idea from uncontacted tribes and peoples in the Amazon and Papua New Guinea?

There's a strong survivorship bias here - the uncontacted tribes tend to be in places that are isolated, and are unsuitable for agriculture or mining. I'm not sure we can infer much about the pre-agricultural lives of people in more normal environments from observing these groups.

Wouldn't we at least be able to derive some data about child mortality and spread of disease and such? Admittedly some of this would be guesswork if they are truly uncontacted and only surveilled and surveyed remotely.

"The sample of premodern populations shows an average modal adult life span of about 72 years, with a range of 68-78 years (Table 4). While modal age at death is not the same as the effective end of the life span, because modal age refers to a peak in the distribution of deaths, it may reflect an important stage in physiological decline. [...]

"Our approach is to assess and analyze available demographic data on extant hunter gatherers and forager-horticulturalists (i.e. peoples who mix hunting and gathering with swidden agriculture). In order to understand the processes that shaped the evolution of our life course, it would be useful to have data on mortality and fertility profiles across populations and over evolutionary time. Given that these data do not exist, we utilize and critically evaluate data on modern groups, as one ‘imperfect lens’ into our past." [1]

[1] Gurven, M., & Kaplan, H. (2007). Longevity among Hunter-Gatherers: A Cross-Cultural Examination. Population and Development Review, 33(2), 321-365. Retrieved from www.jstor.org/stable/25434609

I think you need to move further back. Civilization accounted for a sharp decline in life expectancy due to disease and other factors like extreme agricultural labor. Humans have only gained back what was lost since the industrial and technological revolutions.

Extant hunter gatherers, living without access to modern medicine, have been studied to show life expectancy closer to 70.

Why are you being downvoted? You're talking about relevant periods of history, and providing a much more interesting counterpoint.

I couldn't downvote jly's reply to me even if I wanted to. I didn't upvote it either though. It doesn't cite any evidence and it appeared to be incorrect when I searched for evidence on my own.

See for example: Gurven, M., & Kaplan, H. (2007). Longevity Among Hunter-Gatherers: A Cross-Cultural Examination.

Population and Development Review, 33(2), 321–365.

doi:10.1111/j.1728-4457.2007.00171.x [1]

It was discussed here [2]:

https://old.reddit.com/r/AskHistorians/comments/12o4py/what_...

For the longest living group estimate, 5 year olds can expect to live to ~54, 10 year olds to 55, and even 20 year olds only have a life expectancy of 60. Life expectancy only starts approaching 70 for a hunter-gatherer who survived into his 40s.

This would put life expectancy of young adult hunter-gatherers ahead of that of young adults living in historical agricultural societies, but behind that of those living in highly developed countries in the last several decades. The life expectancy of people living in developed countries today has more than "gained back what was lost since the industrial and technological revolutions."

[1] Enter DOI into sci-hub for full text.

[2] The link to the full text of the PDF in that Reddit post is now broken, which is why I noted the DOI.

Yes, and not only that but current hunter gatherers are restricted to the most marginal environments so they are the worst case.

This is doubtful. All the research I've seen points to very different story. One example:

"the expected annual probability of death for a 65-y-old hunter-gatherer is about 5.3%; in contrast, for 65-y-olds in Japan today, the chance of death is only about 0.8%.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497824/

The figure for Japanese elderly today reflects a life expectancy in the 80s. There's nothing weird about a mortality rate of 5% at 65 corresponding to a life expectancy close to 70.

Aren’t we talking about two different things?

“Maximum lifespan is believed to be under genetic control”

Given modern medicine etc. more people are approaching the maximum lifespan, but we aren’t increasing the maximum.

Some people in the middle ages lived well into their 80s, just not nearly as many as today.

For example, 600 years ago Michelangelo lived to be 88. https://en.m.wikipedia.org/wiki/Michelangelo

There's one popular misconception that everyone died young in Ye Olde Times of Yore. As you note, Michelangelo and some other historic persons with documented lives refute this misconception.

It's also incorrect to attribute shorter historical life expectancy only to infant mortality. That's why I replied to the post by mullingitover. In 1900 Americans had barely even odds of living to age 60 once they had already survived to age 18. Again referencing the Social Security data I originally linked, life expectancy at age 18 increased by 17.3 years (60.3 to 77.6 years), or 29%, over the course of the 20th century.

The maximum life spans documented among the very oldest people are also interesting, and show much smaller gains, but are separate from questions of average life expectancy among infants, children, or young adults.

You're right it's debunked, but even if you take survival rate at age 15 in the Paleolithic era life expectancy was 54 [1]. There were some aristocratic populations that last over 64 at age 21 [1].

[1] https://en.m.wikipedia.org/wiki/Life_expectancy

I've certainly seen that on internet, but I don't known of any real research or hard data, and just go to any old graveyard and work out people's ages. Seems like clickbait debunking rather than real debunking.

I'd say that lots of kids and infants dying in the past dragged down the average to seem comparatively low compared to today. Of those who lived past 18, I'd wager most adults lived almost as long as today unless an infection or simple mechanical injury happened.

Cancer, Alzheimer's, CHD, diabetes' complications and pneumonia gets most people these days. If you live long enough these days, either your heart will give out, your circulatory system will leak and you'll die from shock, you'll get pneumonia or an infection. Finally, the vast majority of end-of-life operations are worse than nothing at all by worsening quality-of-life... hospice is better in most circumstances.

PS: follow the holistic/comprehensive list of preventative lifestyle changes for Alzheimer's so you can go out with your mind as intact as possible and stay fit/able-bodied to where you don't need long-term care (LTC). As an example, the grandpa of that young guy from that show Gold Rush; what a full- and active-life that guy had.

Life expectancy != maximum lifespan

> I thought this idea that humans had short lifespans historically was thoroughly debunked.

Then the Lord said, “My Spirit will not contend with humans forever, for they are mortal; their days will be a hundred and twenty years.”

Genesis 6:3.

I don't know how old Genesis really is, but 2000 B.C. might be a good enough guess. So yeah, pretty thoroughly.

I recently completed my PhD in vertebrate comparative genomics so this is fun to see.

The single most important factor that needs to be accounted for in analyses like these is the correlation between phylogenetic similarity and the trait in question. In short, closely related species will tend to have similar lifespans, and closely related species will tend to have similar CpG density in any fixed genomic region. So the fact that you can predict lifespan from CpG density with enough parameters is unsurprising. You could almost certainly predict lifespan fairly well from any feature measuring phylogenetic similarity -- I would have liked to see some evidence showing that CpG density in these promoters is somehow uniquely suited for the task.

I wonder whether they also looked at body size. Larger species tend to live longer, so it could just be that their regions are just associated with growth.

They did not.

They did mention they were looking at a couple of long lived examples like rockfish that live 200 years vs killifish that live for 1, so this seems to be variable among fish at least. As for mechanism, they were pretty hand wavey but cited reference 33 and mentioned that longer CpG tracts are thought to be protective against spontaneous methylation. Unmethylated CpG islands in promotors are associate with active transcription, especially found in housekeeping genes that are transcribed constantly by definition. Methylating these islands can silence the gene. Makes sense but needs an experiment to know for sure.

So, is this suggesting that humans, as an animal species, are basically "engineered" by evolution to have a 38-year flat part of their MTBF bathtub-curve?

Where I mean "engineered" in the sense that evolution only can only really steer toward adaptive fitness of an organism up until a certain point in its lifetime, that being the point when the organism has done all the breeding they're going to do. Past that point, most things the organism does won't impact the evolutionary cohort of its species, so, turning that around, there will be no adaptations in its genome to help it survive past that point (since, where would they be sourced from?)

That time coming at 38 years for humans would explain a lot, I think. (It makes sense; that's about the oldest average age that humans are willing to continue to have children at.)

when the organism has done all the breeding they're going to do

You could argue that having older and more experienced individuals around might increase chances for survival for everyone. You'd predict that that effect would be especially pronounced in a species that highly relies on culture, like us humans. Indeed the hypothesis was found true for orcas: https://www.pnas.org/content/early/2019/12/03/1903844116

It can be true, but for a gene to reach fixation, it has to be selected for, i.e. organisms without it have to die before breeding.

So this effect might work out if you have a lot of isolated sub-populations, and the ones that live less long suffer extinction, while the ones that live longer go on to eventually reconnect and breed. But it doesn’t really work in a “liquid market”, because free riders without the longevity genes will be just as successful at breeding (due to the existence of the long-lived species members) as the ones with those genes.

Wouldn't evolution steer animals even after breeding if the parents continue to contribute to the success of their children?

If having long lived parents was beneficial to their offspring, evolution will select for longevity well past breeding age. OTOH, if an organism laid eggs and then vanished from it's offspring's lives forever, then it would be hard to see how evolution would select for longevity past the egg laying phase.

Emphatically yes! I believe that may even be the reason humans grow feeble when old - so that the grandparents sit around the fire and nurture the young, teaching and telling stories.

That's why we see menopause in us and in other species like Orcas. Grand parents contribute more food to their grand children without competing to have more kids. I can't find the reference, Google is spammed with diet websites.

You're only 1/4 related to grand children. A strategy of living a long life to help raise a grandchild means that 3/4 of your effort is promoting someone else's genes. Now what if the strategy of those other people is to have many more children, possibly with many different partners, with a relatively diminished per-child investment, reliant on someone like you to help raise those children. Who's going to out-compete whom?

I'm not saying the second strategy is better, just pointing out that the first strategy is self-limiting. Which means we can't even begin to understand the benefits and viability without answering more complex questions; questions we don't yet have answers to.

Also, humans are the only known species, extant or extinct, which exhibits significant non-kin altruism.[1] There's no strong theory for how this emerged. Which means there are some very important dynamics to human evolution (and evolution in general) that we're completely ignorant to--we don't even know what the questions are, let alone the answers.

[1] The most popular mammals used for comparison to humans, bonobos and naked mole rates, are organized as matriarchies--the females are sisters, somewhat like ants and bees. The above-average altruism they exhibit is easily explained by basic Darwinian genetic evolutionary theory.

> You're only 1/4 related to grand children. A strategy of living a long life to help raise a grandchild means that 3/4 of your effort is promoting someone else's genes.

But you are helping to raise 100% of your descendants. I'm not sure it is relevant that your descendants have less genetic material in common with you as you move down the tree.

> Now what if the strategy of those other people is to have many more children, possibly with many different partners, with a relatively diminished per-child investment, reliant on someone like you to help raise those children. Who's going to out-compete whom?

The premise of Idiocracy! In this scenario, though, there could still be benefits of some per-descendant investment. I'm not sure "high investment in few offspring vs. low investment in many offspring" debate really matters to the question of "why stay alive longer than (age of infertility)+(maturation time of offspring)".

I think the answers lie in 'group selection'. Not sure how accepted a theory that is though. An example I've heard (but can't find reference to now) is that the tonsils may serve to kill off sick individuals before they can infect others.

You know, a man who was young indefinitely would have a lot of time to spread his seed...I'd expect such a trait to be strongly selected for if it arose. Unless it had a stiff penalty, maybe more competitive among men, or interbreeding problems?

Right. Think of “breeding” as the complete act of making autonomous organisms. If your children can’t survive without you, then in the evo-bio sense, you haven’t finished “breeding” yet, because the ability of your genes to be passed on still depends on facts about your genome rather than solely on facts about your child’s genome.

Humans take a pretty long time to “breed” compared to most animals, since humans are born pretty non-autonomous compared to most animals. But there still comes a point where the probability of breeding success of a child becomes entirely dominated by the factor of that child’s genes, over the factor of the parent’s.

Also note that, just because this effect exists, doesn’t mean it guarantees that it will be an effect in the direction of longer health-span in every organism. In fact, in many organisms, the organism is wired to die as part of the breeding process, since dying better guarantees success for the offspring! (Some because they no longer compete with their offspring for food; some because their body decays and fertilizes the spawning grounds, leading to a bountiful harvest for their children; etc.)

At a high level, I am very skeptical. Usually when your model does not agree with observations, the problem is with the model. A few things that stand out to me. I have not thought deeply about any of them, so please correct me if I am mistaken about any of these.

> This primary data set contained 252 species from five vertebrate classes [...] We removed humans (Homo sapiens) from the data set as they were listed with a maximum lifespan of 120 years, which does not reflect the variability and the true global average lifespan (60.9–86.3 years)

So why should we trust the rest of this dataset? Garbage in garbage (GIGO) out comes to mind.

> We used promoter sequences centred around the transcription start site (TSS) (-499 to 100 bp of each promoter) in Humans (Homo sapiens) from the EPD as the data set of promoter sequences. [...] Briefly, as described previously, using Basic Local Alignment Search Tool (BLAST) v2.2.31 the promoter sequences were mapped to the single top hit in each species.

This would seem to imply a weird correlation structure between data examples that could pose problems for training/test split and/or linear models. I would also liked to see some QC where they show how well this recovered known (i.e. annotated) promoter regions. Are they picking up false positives? Are they missing stuff?

> The glmnet function was set to a 10-fold cross validation which returns the best performing model. [...] This resulted in a total of 42 promoters for estimate lifespan.

So they're doing post-selection inference, so p-values are suspect. Tibshirani (inventor of Lasso) and Taylor recently released a package for post-selection inference, which I do not see them using here.

> Species were randomly assigned to either a training (176 samples) or testing (76 samples) data set (70/30 split).

Rule of thumb: you usually want about number of example = 10x number of features to avoid overfitting. 42 features seems kind of thin. Even worse when you consider that there might be a correlation between training and test examples imposed by the initial selection of promoter sites using BLAST.

> > We used promoter sequences centred around the transcription start site (TSS) (-499 to 100 bp of each promoter) in Humans (Homo sapiens) from the EPD as the data set of promoter sequences. [...] Briefly, as described previously, using Basic Local Alignment Search Tool (BLAST) v2.2.31 the promoter sequences were mapped to the single top hit in each species.

Measurement error should probably be modeled.

To the experienced data scientists / statisticians here: does this sort of regression analysis between the actual and predicted age seem legit to you?

It seems very weird to me. From what I understand, the p-value tests the hypothesis that the predicted and actual data are correlated, which seems like a very weak way of assessing the reliability of the prediction.

An estimator of the test error seems more relevant, and that's kind of what the R^2 does, but why do an affine regression between predicted and actual value instead of say an RMS error? Isn't this using the test data for parameter-fitting, i.e training?

If the “natural lifespan” of humans ends to be 38 you are using a flawed definition of natural. This also connects to people believe that humans in the past died with 30 latest because the life expectancy was 26 years, ignoring that this is an average heavily influenced by child mortality

> Early humans have been reported to have a maximum life expectancy of 40 years, less than half by modern standards. Similarly, in chimpanzees the lifespan was estimated at 39.7 years. The maximum longevity of a chimpanzee in the wild is thought to be of a 55 years old female, however it is reported that many live to approximately 40 years of age.

It seems like what we’re really seeing here is the similarity in lifespan between our earliest human ancestors and other primate species.

The earliest humans would not yet have had access to consistent shelter, fire or tools/weapons and these developments carried with them enormous benefits with respect to health and comfort.

Off topic, but based on the discussions here.

I'm seeing a lot of discussion here about how the lifespan of humans (not counting infant and teen mortality rates) may not have improved much in the last thousand years. As a tangential question, does that mean all our medical progress has a) improved infant mortality and b) counteracted the unhealthiness of modern life, and not done much for us beyond that?

From what I've read that's right. Kids don't die on nearly the same scale, likewise mothers giving birth.

Nutrition has gotten better, which helps immune system strength.

We know what causes a lot of diseases and can protect against their spread. Both reactively in terms of illnesses people get and in terms of prevention such as vaccines and warnings about smoking.

Even then there are records of famous ancient people like Egyptian kings who lived to what we'd still consider a ripe old age now.

No comments about dog lifespans? Come on genetic engineering, give me a Labrador that lives 20 years and doesn’t shed.

Get a hairless cat, similar personality actually

previously https://news.ycombinator.com/item?id=21773562

Can we please repeal and replace the title of this with “A genomic predictor of lifespan in vertebrates” (aka the real title) ?

Yes. The submitted title was "Humans have a natural lifespan of only 38 years", which broke the site guidelines. They ask: "Please use the original title, unless it is misleading or linkbait; don't editorialize." We've reverted the title now.

https://news.ycombinator.com/newsguidelines.html

thumbs up

That article title is crap.

Edit: the title is fixed now.

I agree, that title is awful given the actual link.

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