Hum vs. anthr
Other vs. anthr
The results obtained with respondent subgroups based on total number of authored peer reviewed publications and total number of authored popular science publications are not shown, because they were not associated with significantly different ( p < .05) means in any comparisons.
*** p < .001; ** p < .01; * p < .05.
Overall scientific experience (as measured with the number of scientific publications authored) had no effect on the scores given to either the dryland or the water‐related hypotheses (Table 2 ). However, the more knowledge the respondents had on human evolution specifically (self‐assessed familiarity with the hypotheses, number of scientific publications on human evolution or experience in teaching human evolution), the lower the scores they gave to the water‐related hypotheses. Among biologists, those who knew more about human evolution were more critical than the less knowledgeable ones, and (paleo)anthropologists were more critical than human biologists with the same self‐assessed knowledge level.
When the dryland hypotheses were split into two groups depending on whether they were based on behavioral arguments or environmental adaptation, both groups obtained rather similar results. The main difference was that the behavioral hypotheses received somewhat higher average credibility scores, which reflects the fact that 10 of the 12 most popular hypotheses were based on behavior (on the other hand, so were the four least popular hypotheses).
To visualize the differences in opinion among the (paleo)anthropologists and representatives of other fields, we repeated the ordination of the hypotheses for each of the four respondent groups separately. In accordance with the fact that most respondents were biologists, the ordination based on the biologists’ data only (Figure 2 c) was very similar to the ordination based on all respondents (Figure 2 a). The ordination based on (paleo)anthropologists’ views (Figure 2 b) differed especially in relation to the hypotheses for bipedalism: Hypotheses that explained bipedalism by foraging, tool use, or carrying were very far removed from the main cloud and toward the opposite side than the water‐related hypotheses. In addition, the average credibility scores given to the water‐related hypotheses were among the lowest of any hypotheses. This contrasted with the situation in the ordination based on human biologists’ data (Figure 2 d), in which the water‐based hypotheses had intermediate credibility scores.
The hypotheses differed clearly from each other in the frequencies of different credibility scores, but there were some similarities in the overall pattern among those six traits for which three or more hypotheses were evaluated (Figure 4 ). None of the hypotheses received the “very likely” score from more than 46% of the respondents, but most traits had at least one hypothesis that was considered “very likely” by more than 23% and likely (either “very likely” or “moderately likely”) by 72%–90%. Many of the intermediately popular hypotheses divided the respondents rather evenly between those who found them likely and those who found them unlikely (the latter referring to the scores “very unlikely” and “moderately unlikely” combined).
Credibility scores given by survey respondents to hypotheses that aim to explain the evolutionary origin of specific human traits. The hypotheses are sorted in order of decreasing popularity as estimated by the percentage of respondents who scored them likely (i.e., either “very likely” or “moderately likely”). Descriptions of the hypotheses as they were given in the survey are shown in Table 1
A causal relationship between articulate speech and descended larynx was accepted by most respondents, but there was no consensus on the direction of the causality. That the larynx descended because this was required by articulate speech was found likely by 84% and very likely by 43%. At the same time, that the evolution of speech was triggered by the descended larynx was found likely by 61% and very likely by 18%. In fact, 36% of the respondents scored both directions as equally likely.
Traits in the category “other” had only one explanatory hypothesis each in the survey, and this was water‐related. All of these hypotheses received many more “very unlikely” than “very likely” scores. However, four hypotheses (that baby swimming, profuse sweating, diving ability, and magnitude of diving reflex evolved as adaptations to a semi‐aquatic way of life) received so many “moderately likely” scores that the percentage of respondents who found them likely was slightly larger than the percentage who found them unlikely (Figure 4 ).
Details on how the hypotheses were scored by respondents representing different fields of expertise are shown in Figure 5 . In accordance with the statistical test results, most hypotheses received rather similar scores from respondents of all fields of expertise. However, (paleo)anthropologists were clearly more critical than representatives of the other fields in relation to several hypotheses, including: that nakedness evolved to avoid ectoparasites, that the big brain evolved because warfare caused pressure for higher intelligence, and that any traits evolved as adaptations to swimming or diving.
Frequencies of credibility scores given to hypotheses aiming to explain different traits (columns) by respondents of different fields of expertise (rows). In each panel, the answers are, from left to right, “very likely,” moderately likely,” “no opinion,” “moderately unlikely,” and “very unlikely.” Hypotheses that have been included in the aquatic ape hypothesis are shown in shades of blue and green. Those dryland hypotheses for which the opinions of anthropologists and other expertise groups clearly diverged are shown in magenta. The other hypotheses are in shades of brown, with darker colors given to hypotheses that received higher average credibility scores in the survey
There was a lot of variation among the traits in how many of the proposed explanations the respondents found convincing (Figure 6 ). For any one trait, 33%–64% of the respondents did not find any of the proposed hypotheses “very likely,” while 19%–38% found exactly one and 8%–45% more than one. Ten respondents (0.8%) explained that they did not score any of the hypotheses as likely, because they do not believe that humans have evolved at all (most of them explicitly referred to special creation by God).
The number of hypotheses (colors) proposed to explain each human trait (rows) that each respondent found very likely (left panel) or likely (either very likely or moderately likely; right panel). The total number of hypotheses included in the survey is shown after the name of each trait
The survey asked respondents’ opinions on twenty critical arguments that have been presented against the aquatic ape hypothesis. For most arguments, the modal response was “no opinion,” especially among those 43% of the respondents who had never heard of AAH before. Nevertheless, some arguments were clearly more frequently agreed with than others (Figure 7 and Table 3 ). The most widely accepted critique was that not all aquatic mammals have naked skin, so hairlessness cannot be considered an aquatic adaptation. In the other extreme, less than 3% of the respondents fully agreed and less than 12% mostly agreed with the critique that AAH is unscientific or not worthy of attention for the reasons given; in most cases, the number of respondents who strongly disagreed with these critiques was larger than the number who mostly or fully agreed.
The degree to which respondents representing different expertise fields agree with critique presented against the aquatic ape hypothesis. The full description of each point of critique can be found in Table 3
Points of critique presented against the aquatic ape hypothesis (AAH). The abbreviations are used in Figure 7 , and the full text is copied verbatim from the survey
Abbreviation | Critique |
---|---|
Hairy aquatics | Not all aquatic mammals have naked skin, so hairlessness cannot be considered an aquatic adaptation. |
Not parsimonious | AAH is less parsimonious than other proposed hypotheses: It has to explain both how human traits evolved in water, and how they were retained after return to land. |
Unnecessary | AAH is not needed, because all human traits can be explained by terrestrial scenarios. |
Coincidence | Humans may be similar to aquatic mammals in some traits, but this is only a coincidence and has no evolutionary relevance. |
No skeletal adaptations | AAH is not supported by fossil evidence, because this shows no skeletal adaptations to an aquatic environment. |
Determinism | A major problem with AAH is that it is based on extreme environmental determinism. |
Nonaquatic fossils | AAH is contradicted by the fossil record, because this suggests a permanently nonaquatic environment. |
Less consistent | AAH is internally less consistent than other proposed hypotheses. |
Apes swim | According to AAH, humans should swim better than apes and have more streamlined bodies, but they do not. |
Not enough time | There has not been enough time for an aquatic phase. |
Comparative anatomy | AAH is merely an exercise in comparative anatomy, not a scientific hypothesis. |
Conflicts evolution | AAH conflicts with what is known about evolutionary processes in general. |
Timing unknown | AAH lacks credibility, because its proponents do not agree on when and where the supposed aquatic phase took place. |
Simplistic | AAH is too simplistic to be taken seriously. |
Not peer‐reviewed | AAH can be ignored, because it was not published in a peer‐reviewed journal, and because it is mostly discussed in forums other than scientific journals. |
False evidence | AAH lacks credibility, because the evidence presented in its favor is false. |
Not professionals | AAH can be ignored, because its main proponents are not professionals in the field of human evolution. |
Pseudoscience | AAH is pseudoscience comparable to creationism. |
Cannot predict | AAH is unscientific, because it cannot make predictions. |
Feministic | AAH is unscientific, because it has been used in feministic argumentation. |
The main results of our survey can be summarized as follows: (1) There was no general agreement among the respondents on why any of the uniquely human traits have evolved: None of the proposed hypotheses was universally either accepted or rejected. (2) For any individual trait, the percentage of respondents who found none of the hypotheses “very likely” was between >30% (bipedalism) and >65% (nakedness). (3) In general, opinions on the credibility of the hypotheses were independent of a person's background (gender, age, field of expertise, degree of scientific experience), but (paleo)anthropologists were clearly more critical than representatives of other fields. (4) The hypotheses that mention adaptation to swimming or diving as an explanatory factor were found much less credible by (paleo)anthropologists and slightly more credible by human biologists than by biologists and representatives of other fields. (5) Most respondents were critical about the aquatic ape hypothesis (AAH), but only a small minority considered it to be unscientific.
Of course, all conclusions based on the survey data must be considered tentative only, because the response rate was very low, and it is possible that the results are biased. Members of some subgroup might have been more likely to respond than members of some other subgroup, and the average credibility scores given to the different hypotheses by the respondents may not be representative of the opinions of all scientists in the background population. However, it is unlikely that a lack of general agreement on the drivers of trait evolution or such a clear difference in opinion between (paleo)anthropologists and others could have emerged just as a result of biased sampling.
Our results did not reveal a set of explanations that would collectively provide a coherent and popular scenario for the origin of all (or even many) human traits. Indeed, some of the hypotheses that had almost equal and rather high average credibility scores explained the same trait, whereas for other traits, no hypothesis emerged as particularly popular. Against this background, it is interesting that almost half of the respondents fully or mostly agreed with the statement that the aquatic ape hypothesis “is not needed, because all human traits can be explained by terrestrial scenarios”.
The lack of agreement on why humans evolved the traits we have today is very obvious in our results: No hypothesis was universally accepted, and for most traits, there were several almost equally popular alternative hypotheses rather than one that would generally be considered superior to the others. None of the hypotheses received the score “very likely” from more than half of the respondents or obtained an average credibility score higher than 4.26 (of 5). For hairlessness, the most popular hypothesis was thought to be “very likely” by only 16% of the respondents, and its average credibility score (3.48) was closer to 3 (which is the limit between being considered more likely than unlikely) than to 4 (moderately likely). In addition, for only two of the traits (subcutaneous fat layer and descended larynx), the most popular hypothesis was found at least moderately likely by almost all respondents at the same time as the next most popular hypothesis was found clearly less likely. This may partly reflect the fact that fewer alternative hypotheses have been proposed for these traits than for many of the others included in the survey.
Importantly, lack of agreement did not reflect just ignorance on the topic among nonspecialists, because the responses were, in general, very similar between anthropologists and respondents representing other fields of science. In fact, anthropologists were even more skeptical about all hypotheses than representatives of the other fields were. In other words, outsiders were slightly more convinced that the proposed hypotheses are plausible than those who work in the field. Maybe anthropologists (especially paleoanthropologists) are more systematically trained to be wary of just‐so‐stories (explanations of past events and processes backed up by little or no evidence) than students in nearby fields are. It is also possible that outsiders are somewhat less likely to question hypotheses proposed within an unfamiliar field. This could be because they do not feel qualified to do so, or because they have not heard of the debates that draw attention to the weaknesses of the hypotheses.
Our results conform with the widespread belief that professionals in the field of human evolution are more critical toward the aquatic ape hypothesis (AAH) than outsiders are (Langdon, 1997 ; Bender et al., 2012 ; see also nonscientific sources such as Hawks, 2005 ; Moore, 2012 and Wikipedia: Aquatic Ape Hypothesis: Talk). However, this did not seem to be due to overall scientific ignorance, because how respondents assessed the credibility of the hypotheses proposing adaptation to swimming or diving was independent of both their overall scientific experience level and how they assessed the credibility of the other hypotheses. Interestingly, those whose main field of expertise is human biology had the most positive attitudes toward the water‐related hypotheses, giving them an average credibility score that was as much as 0.9 units higher (on a 1–5 scale) than the average score given by (paleo)anthropologists.
The difference in average opinion between (paleo)anthropologists and other scientists can be interpreted in two opposite ways. On the one hand, those who know the field of human evolution best may be best positioned to make a justified evaluation of the validity of the alternative hypotheses. On the other hand, prior knowledge may induce one to reject unconventional hypotheses offhand merely because they challenge the established paradigms of a field (Bender et al., 2012 ; Klayman, 1995 ). Obviously, the two interpretations lead to opposite conclusions on whether or not the critical attitude of the (paleo)anthropologists can be taken as evidence that AAH is flawed. In our survey, a vast majority of the respondents who had an opinion on the issue disagreed with the statement that AAH can be ignored because its main proponents are not professionals in the field of human evolution. This was the case both overall and within each field of expertise separately, although the proportion of respondents who agreed with the statement was higher among (paleo)anthropologists than among representatives of the other fields.
In this context, it is also interesting that the respondents’ assessment of the credibility of the water‐related hypotheses did not depend on the number of scientific papers they had authored. This indicates that established scientists are no more likely to reject or accept these hypotheses than junior scientists are—unless their scientific experience relates directly to the field of human evolution. A vast majority of the respondents disagreed with the critique that AAH is unscientific. Of course, this does not mean that they would consider the explanations proposed by AAH to be correct, and indeed, all the hypotheses related to AAH received relatively low credibility scores (although not as low as the least popular dryland hypotheses).
If, for the sake of argument, we accept the most popular explanation for each trait to be the correct one, a scenario of evolution by internal drive emerges: The large brain evolved because complex social organization required higher intelligence, the subcutaneous fat layer evolved to serve as an energy reserve for the developing brain, articulate speech evolved because there was social pressure for elaborate communication, the larynx descended because this was required by articulate speech, bipedalism evolved to make the use of tools and weapons easier, and nakedness evolved to avoid overheating when hunting. For most traits, the next most popular explanation was not far behind in popularity. Most of these were also based on inherent drivers, but sometimes in the opposite temporal sequence (e.g., articulate speech was triggered by the descended larynx; large brain evolved because it was required by articulate speech). We found this result disturbing, because the overwhelming popularity of hypotheses based on inherent drivers gives the impression that human evolution is generally thought to have been goal‐directed. This would be in conflict with the current understanding (explained in every evolutionary biology textbook) that evolution has no foresight.
Overall, the survey revealed no general agreement among the respondents: None of the proposed hypotheses on why specific uniquely human traits have evolved was universally either accepted or rejected. Nevertheless, identifying and quantifying what is not generally known and agreed upon can be useful in itself, as it may help to focus future research on answering the most important open questions. Clearly, there is still a long way to go before the question “why are humans so different from other primates” has been answered in a comprehensive and generally satisfactory way.
Conflict of interest.
None declared.
HT designed and conducted the survey and led the writing. All authors discussed the results and planned the data analyses together. The R code used to analyze the data and draw the figures was written by MT with contributions from JT.
Acknowledgments.
We thank Carlos Peña for writing the code to extract respondents’ email addresses from the Internet; Mirkka Jones, Kalle Ruokolainen, and Timo Vuorisalo for comments that helped to improve the survey questions; and Jouko Tuomisto for comments on the manuscript.
Tuomisto H, Tuomisto M, Tuomisto JT. How scientists perceive the evolutionary origin of human traits: Results of a survey study . Ecol Evol . 2018; 8 :3518–3533. https://doi.org/10.1002/ece3.3887 [ PMC free article ] [ PubMed ] [ Google Scholar ]
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Wanting to understand who we are, where we come from and how we evolved is part of what makes us human.
This an exciting time to be examining human evolution. Intriguing fossil and archaeological discoveries, combined with innovative techniques and DNA research, are transforming scientists' understanding of our ancient past.
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The Y chromosome in primates — including humans — is evolving much more rapidly than the X chromosome, new research on six primate species suggests.
For instance, humans and chimpanzees share upwards of 98% of their DNA across the whole of the genome, but just 14% to 27% of the DNA sequences on the human Y chromosome are shared with our closest living relatives.
The finding surprised scientists, given that humans and chimpanzees diverged just 7 million years ago — a blip in evolutionary terms.
"I expect my genome to be very different to that of bacteria or insects because a lot of time has elapsed, evolutionarily speaking," study co-author Brandon Pickett , a postdoctoral fellow at the National Human Genome Research Institute (NHGRI) at the National Institutes of Health, told Live Science. "But from other primates, I expect it to be pretty similar."
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It's not clear exactly why the Y chromosome is evolving so rapidly. For starters there is only a single copy of the Y chromosome per cell — in primates, females carry two copies of the X chromosome, while males carry an X and a Y chromosome ––the Y chromosome plays a critical role in sperm production and fertility. Having only a single copy of the Y chromosome presents a vulnerability ––if changes happen to occur, there is no second chromosome to act as a backup.
And changes are likely to occur due to something called mutation bias. The Y chromosome may be so prone to change because it generates many sperm. This requires lots of DNA replication. And every time DNA is copied, there's a chance for mistakes to creep in.
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Scientists have previously sequenced the primate genome for all 16 representative families .
In the new study, published May 29 in the journal Nature , scientists compared the sex chromosomes of five great ape species — chimpanzees ( Pan troglodytes ), bonobos ( Pan paniscus ), western lowland gorillas ( Gorilla gorilla gorilla) and Bornean and Sumatran orangutans ( Pongo pygmaeus and Pongo abelii ) — and one more distantly related to humans, siamang gibbons ( Symphalangus syndactylus ).
The team studied the chromosomes using telomere-to-telomere (T2T) sequencing. T2T can accurately sequence repetitive elements, including the protective telomere "caps" of chromosomes that have proven difficult to read in the past, Pickett said. The researchers used computing software to make comparisons between the sequencing results, by creating alignments to reveal which parts of the chromosome had changed and which parts had stayed the same.
The chromosomal X and Y sequences of each of the six species were also compared to the human X and Y chromosome, already sequenced in an earlier study with the T2T method.
The findings revealed that across all the studied species, the Y chromosome evolved rapidly. Even species in the same genus have very different Y chromosomes to one another. For instance, chimpanzees and bonobos diverged just 1 million to 2 million years ago, yet there is a dramatic difference in their Y chromosome lengths, said Christian Roos , a senior scientist at the Primate Genetics Laboratory, German Primate Center, who was not involved in the study.
In some cases the difference in length — caused by chromosome losses or duplications that occur when DNA is copied — amounted to up to about half of the observed differences. For example, the Y chromosome from the Sumatran orangutan is twice as long as the gibbon's Y chromosome.
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In contrast, the study found that the X chromosome was highly conserved across the primate species, as might be expected for a structure with a critical role in reproduction.
One reason the Y seems to have thrived despite such a high rate of mutation is that across all the studied species, it contains stretches of highly repetitive genetic material, such as palindromic repeats, where the sequence reads the same forward and backward. Nestled within these stretches of repeating DNA are genes. So the repeated DNA may safeguard important genes from replication mistakes and thereby preserve essential biological material, the researchers wrote in their paper.
The study did have limitations though; it looked at only a single representative for each primate species, and it couldn't say how much the Y chromosome would vary within animals of the same species, Pickett said.
Nicola Williams holds a PhD in the History of Science from the University of Leeds, U.K. and currently works as a science writer across an array of subject areas broadly spanning, but not limited to, biology, physics, medicine and technology.
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Humans began to rapidly accumulate technological knowledge through social learning around 600,000 years ago.
Stone tools that become increasingly more complex over the course of 3 million years. Left: First time period studied — Oldowan core, Koobi Fora, Kenya (below baselines). Center: Second time period studied — Acheulean cleaver, Algeria (around baseline). Right: Characteristic of 600,000 year ago technology — Levallois core, late Pleistocene Algeria. Image credits: (left) Curry, Michael. 2020. Oldowan Core, Koobi Fora. Museum of Stone Tools. Retrieved June 10. From: https://une.pedestal3d.com/r/DGHMTdkn4_; (middle) Curry, Michael. 2020. Acheulean Cleaver, Morocco, Koobi Fora. Museum of Stone Tools. Retrieved June 10. From: https://une.pedestal3d.com/r/JMVajqyz29; (right) Watt, Emma. 2020. Levallois Core, Algeria. Museum of Stone Tools. Retrieved June 10. From: https://une.pedestal3d.com/r/JMVajqyz29.
Each of us individually is the accumulated product of thousands of generations that have come before us in an unbroken line. Our culture and technology today are also the result of thousands of years of accumulated and remixed cultural knowledge.
But when did our earliest ancestors begin to make connections and start to build on the knowledge of others, setting us apart from other primates? Cumulative culture — the accumulation of technological modifications and improvements over generations — allowed humans to adapt to a diversity of environments and challenges. But, it is unclear when cumulative culture first developed during hominin evolution.
A study published this week in the Proceedings of the National Academy of Sciences journal by Arizona State University researcher Charles Perreault and doctoral graduate Jonathan Paige concludes that humans began to rapidly accumulate technological knowledge through social learning around 600,000 years ago.
“Our species, Homo sapiens, has been successful at adapting to ecological conditions — from tropical forests to arctic tundra — that require different kinds of problems to be solved," said Perreault, a research scientist with the Institute of Human Origins and an associate professor with the School of Human Evolution and Social Change . “Cumulative culture is key because it allows human populations to build on and recombine the solutions of prior generations and to develop new complex solutions to problems very quickly.
"The result is, our cultures — from technological problems and solutions to how we organize our institutions — are too complex for individuals to invent on their own.”
To investigate when this technological turn may have begun and to explore the origin of cumulative culture, Paige and Perreault analyzed changes in the complexity of stone tool manufacturing techniques across the past 3.3 million years of the archaeological record.
As a baseline for the complexity of stone tool technologies achievable without cumulative culture, the researchers analyzed technologies used by nonhuman primates — like chimpanzees — and stone tool manufacturing experiments involving inexperienced human flintknappers and randomized flaking.
The researchers broke down the complexity of the stone tool technologies by the number of steps (procedural units, or PUs) that each tool-making sequence involved.
The results suggested that from around 3.3 to 1.8 million years ago — when australopiths and earliest Homo species were around — stone tool manufacturing sequences remained within the range of the baselines (1 to 6 PUs). From around 1.8 million to 600,000 years ago, manufacturing sequences began to overlap with and slightly exceed the complexity baseline (4 to 7 PUs). But, after around 600,000 years ago, the complexity of manufacturing sequences rapidly increased (5 to 18 PUs).
“By 600,000 years ago or so, hominin populations started relying on unusually complex technologies, and we only see rapid increases in complexity after that time as well. Both of those findings match what we expect to see among hominins who rely on cumulative culture,” said Paige, a postdoctoral researcher at the University of Missouri and an ASU PhD graduate.
Tool-assisted foraging may have been the impetus for the earliest beginning of the evolution of cumulative culture. Early hominins, 3.4 to 2 million years ago, likely relied on foraging strategies that require tools — like accessing meat, marrow and organs — leading to changes in brain size, lifespan and biology that set the stage for cumulative culture.
While other forms of social learning may have influenced tool-making, it is only in the Middle Pleistocene when there is evidence for rapid increases in technological complexity and the development of other kinds of new technologies.
The Middle Pleistocene also shows consistent evidence of controlled use of fire, hearths and domestic spaces, likely essential components of the development of cumulative culture. Other kinds of complex technologies also developed in the Middle Pleistocene, including wooden structures constructed with logs hewn using hafted tools, which are stone blades affixed to wooden or bone handles.
This all suggests that cumulative culture arose near the beginning of the Middle Pleistocene epoch, possibly predating the divergence of Neanderthals and modern humans.
Published article: 3.3 million years of stone tool complexity suggests cumulative culture began during the Middle Pleistocene . Jonathan Paige and Charles Perrealt. Proceedings of the National Academy of Sciences .
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Evolution, as related to genomics, refers to the process by which living organisms change over time through changes in the genome. Such evolutionary changes result from mutations that produce genomic variation, giving rise to individuals whose biological functions or physical traits are altered. Those individuals who are best at adapting to their surroundings leave behind more offspring than less well-adapted individuals. Thus, over successive generations (in some cases spanning millions of years), one species may evolve to take on divergent functions or physical characteristics or may even evolve into a different species.
Evolution. Studying the science of evolution can completely transform our understanding of the subject of history. Evolution is, in a way, the history of all living organisms on Earth. And the timescale for appreciating that history is just so many orders of magnitude greater than what we can understand from the study of human history alone. It's actually humbling to situate human experience against that backdrop of millions of years of gradual change to the genome, millions of years of activity that took place on Earth prior to humans coming onto the scene.
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Have living things always existed in their present form, or did they evolve? And if evolution occurred, was a divine hand at play?
Measuring public opinion on evolution has never been an easy task for survey researchers. With Americans’ views on the topic tapping into the highly charged realms of religious conviction and scientific knowledge, question wording becomes extremely important. For this reason, in recent years, Pew Research Center has experimented with different ways of asking about evolution and studied whether these variations affect the public’s responses. And because they do, the Center is moving toward a revised wording.
First, a bit of survey history: For a decade and a half, the Center asked Americans what they believe about the origins of humankind, most often in a two-step process. An initial question asked respondents whether they think humans and other living things have evolved over time – in line with Charles Darwin’s theory of evolution – or whether they believe humans have existed in their present form since the beginning of time, as in the Book of Genesis’ creation story. Those who said they accept the idea of evolution then have been asked a second question: whether they think evolution has occurred due to natural processes such as natural selection, or due to processes that were guided or allowed by God.
Recently, however, the Center conducted a survey in which respondents were randomly assigned to be asked about evolution in one of two different ways. Half of the respondents were asked about evolution in a two-step process much like the one described above. The other half of respondents were asked a single question about their views on evolution and given three response options: “Humans have evolved over time due to processes such as natural selection; God or a higher power had no role in this process”; “Humans have evolved over time due to processes that were guided or allowed by God or a higher power”; or “Humans have existed in their present form since the beginning of time.”
The data show that respondents in the latter group (those who receive a single question with three options) are more likely than those in the former group to say evolution has occurred. Overall, eight-in-ten in the single-question group say humans have evolved over time (and just 18% say humans have always existed in their present form), while only two-thirds of those who receive the older, two-step approach say humans have evolved (and 31% express the creationist view).
Put more simply, our estimate of the share of Americans who reject evolution and express a creationist view drops considerably (from 31% to 18% of U.S. adults) when respondents are immediately given the opportunity to say God played a role in human evolution. The effect of the different question wording is especially pronounced among white evangelical Protestants and black Protestants.
The experimental findings illustrate why testing multiple ways of asking about evolution is necessary and important. For some people, views about the origins and development of human life are bound up with deeply held religious beliefs. Pew Research Center’s goal in designing questions on this topic is to allow respondents to share their thoughts about both the scientific theory of evolution and God’s role in the creation and development of life on Earth – and to do so in a way that does not force respondents to choose between science and religion. Indeed, the data show that many Americans believe that life on Earth has evolved over time AND that God or a supreme being played some role in the evolutionary process.
In the future, Pew Research Center intends to use this new, three-option approach to asking about evolution in much of its U.S.-based survey research – though the older, two-step approach may continue to work well in certain international contexts (for example, in countries where views about evolution are less closely bound up with religious beliefs than is the case in the U.S.) or for monitoring long-term trends in the United States. The results of the new experiment indicate that there are some people who do believe that humans have evolved over time, but who, for whatever reason, did not say so in our traditional method of asking about the topic. Perhaps without the opportunity to immediately connect evolution to God, some religious respondents may be concerned that expressing belief in evolution places them uncomfortably on the secular side of a cultural divide.
The results of the survey also show that devising survey questions that enable respondents to register nuance in their views about these subjects is very important – and very challenging. Prior to this most recent experiment, the Center tested various versions of the two-step process to asking about evolution. In one line of testing, we varied the survey context (that is, the questions that immediately precede the evolution questions). In another line of testing, we varied whether the questions asked about the evolution of “ humans and other living things” or “ animals and other living things.”
What follows below is a brief history of the way the Center has asked about evolution.
The first time Pew Research Center asked about evolution, in 2005 , the evolution questions were preceded with up to two questions about belief in God. Respondents were asked whether they believe in God, a higher power or universal spirit (but not God), or neither God nor a higher power or universal spirit. Those who said they believe in God or a higher power were asked if they believe that this entity “was responsible for the creation of life on Earth.”
Then, all respondents were asked the following question, which included the wording that would become our core language for evolution questions over the next decade: “Some people think that humans and other living things have evolved over time. Others think that humans and other living things have existed in their present form since the beginning of time. Which of these comes closest to your view?”
[do you think that]
Why begin a survey module about evolution with questions about belief in God? Researchers were concerned that questions about evolution may have become so caught up in contentious debates about religion, culture and politics that simply asking about evolution outright might lead to erroneous results. Religious people who believe both that evolution has occurred and that God played a role in it might nevertheless – when asked cold – choose the creationist option simply as a way of registering their belief that God exists, and not because they truly reject evolution. Without having first been given the chance to stipulate that they believe God exists and played a role in the creation of life on Earth, some respondents may have seen it as socially undesirable to say they believe humans have evolved over time.
Overall, the 2005 survey found that roughly half of U.S. adults said humans have evolved over time, including 26% who said evolution was due to natural processes, and 18% who said it was guided by a supreme being. Four-in-ten said humans have existed in their present form since the beginning of time, and an additional 10% either were not sure or declined to answer the question.
The following year, the Center again explored people’s views on evolution. The 2006 survey included an experimental test of the premise that asking about belief in God would affect respondents’ answers to the ensuing questions on evolution. Half of the survey’s respondents were randomly assigned to receive the belief-in-God questions before the evolution questions, while the other half of respondents did not receive the belief-in-God questions.
Analysis of the data showed that respondents answered the evolution question series similarly, regardless of whether they were first asked about their belief in God. Since the experimental test showed that asking about belief in God had no impact on the way respondents answer questions about evolution, all Pew Research Center surveys conducted since 2006 have omitted the introductory questions measuring beliefs about God.
The Center asked a very similar, two-step battery of evolution questions three years later . The survey results appeared to show an increase of 10 percentage points in the share of Americans who say they believe evolution has occurred, from 51% in 2006 to 61% in 2009. However, researchers were concerned that responses to the 2009 question may have been influenced by the fact that the entire 2009 survey was about scientific topics.
Specifically, people who are most interested in scientific topics may have been more likely to participate in the survey. Such individuals may also believe in evolution at higher rates than those who are not so interested in scientific topics, thus inflating the survey’s estimate of the share of the public that believes evolution has occurred.
It is also possible that a slight change to the wording of the question between 2006 and 2009 could have affected the results. In 2005 and 2006, the first question in the series read as follows: “Some people think that humans and other living things have evolved over time. Others think that humans and other living things have existed in their present form since the beginning of time. Which of these comes closest to your view?” Beginning in 2009, the question was simplified to ask “Which comes closer to your view? Humans and other living things have evolved over time, OR humans and other living things have existed in their present form since the beginning of time.” 1 The original wording may have lent equal legitimacy to both viewpoints by telling respondents that there are people on both sides of the debate; this may have nudged some to the creationist response.
As a result of the different survey context and the slight change in question wording, Pew Research Center did not report the 2009 results as the continuation of a trend that began in 2005. Instead, the earlier results were included alongside the 2009 findings only as a “trend for comparison” – as an indication that there may have been some change in sentiment between 2006 and 2009, but without making a direct, apples-to-apples estimate of the magnitude of the change.
Between 2013 and 2014, Pew Research Center asked the two-step evolution question series four more times. On all four occasions, the share of those who said they believe humans have evolved over time fell between 60% and 65%.
In the 2014 U.S. Religious Landscape Study (the last telephone survey in which the Center asked the traditional, two-step series of questions about evolution), the data show that belief in evolution is more common among college graduates (73%) than among those with lower levels of educational attainment (62% among those with some college education, 53% among those with a high school diploma or less education). Belief in evolution is also more prevalent among young people (72% among adults under the age of 30) than among older adults (52% among those ages 65 and older), and somewhat more common among men than women (65% vs. 58%).
Among religious groups, belief in evolution peaks among self-described atheists (95% of whom say they believe humans and other living things have evolved over time) and agnostics (96%). Roughly eight-in-ten or more Buddhists (86%), Jews (81%) and Hindus (80%) also say they believe in evolution, as do smaller majorities of Catholics (66%) and mainline Protestants (65%) – though members of these Christian traditions are much more likely than religiously unaffiliated people and members of most non-Christian faiths to say they believe God played a role in guiding the evolutionary process.
Among members of evangelical Protestant denominations, the balance of opinion leans in the opposite direction – 57% of evangelicals said in the 2014 telephone survey that humans and other living things have existed in their present form since the beginning of time, compared with 38% who said they believe humans have evolved over time. And members of historically black Protestant denominations were divided about evenly between those who believe in evolution (50%) and those who do not (45%). Statistical analysis shows that evangelicals and people who belong to historically black Protestant denominations are less likely than those in many other religious groups to believe in evolution even after accounting for different levels of educational attainment.
As noted at the outset of this report, our recent experiment found that including an immediate option to link God to evolution makes a substantial difference in the responses given by white evangelicals and black Protestants. For details, see “ How highly religious Americans view evolution depends on how they’re asked about it .”
In 2013, Pew Research Center experimented with the wording of the standard question about evolution. A random group of respondents was asked about the evolution of “ humans and other living things,” while other respondents were asked about the evolution of “ animals and other living things.”
The survey found that white evangelical Protestants were more likely to say animals and other living things have evolved over time (41%) than they were to say the same about humans (27%). Among white mainline Protestants, the opposite was true: More said humans evolved (78%) than animals (66%). The experiment found no significant differences in the way black Protestants, Catholics and religiously unaffiliated respondents answered the questions.
Taken together, the findings presented here show that asking questions about the origin and development of life on Earth can be a complicated undertaking – perhaps especially in a country like the United States, where the public’s attitudes about the scientific theory of evolution often are bound up with their religious convictions. What may seem like small differences in question wording can have a major impact on survey estimates of the share of the public that believes in a naturalistic account of human development, a creationist view or something in between – an evolutionary process guided or at least allowed by God or a supreme being. Pew Research Center has been committed to innovation on these kinds of questions to try to capture public opinion in its full complexity, and the Center will continue to experiment and report the results transparently.
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If trillions of tiny bits of consciousness are floating around inside you, it could change how we think about life.
The reason for such cooperation comes down to a cellular form of intelligence, says evolutionary biologist and physician William B. Miller, Ph.D. He’s co-author of the book, The Sentient Cell: The Cellular Foundations of Consciousness , published in January 2024, which proposes a radical new way of thinking about some of life’s tiniest components .
Miller is among a small but growing group of scientists who believe we should no longer think of cells as passive robots that automatically follow a code of instructions, carrying out orders from our genome like mindless drones. Instead, they say, the roughly 37 trillion cells that make up our own bodies are conscious —and that life and consciousness began at the same time.
It’s a revolutionary idea, Miller tells Popular Mechanics , but assuming cells have a form of consciousness can give us a better understanding of complex processes. These include cellular communication and decision-making, and even the motivation behind an embryonic cell specializing into a specific organ. While it’s not widely accepted among scientists, this concept of “ existential consciousness ” will profoundly transform the way we approach cellular bioengineering problems like tissue regeneration, provide a different perspective on finding cures for diseases like cancer , and even help us survive on Mars, Miller says.
Now, in a May 2024 paper published in the peer-reviewed journal Progress in Biophysics and Molecular Biology, Miller and his fellow authors argue that random chance did not govern the concept of natural selection; that’s what the 1850s naturalist Charles Darwin, known for establishing the theory of evolution, thought. Instead, the authors contend that a form of cellular consciousness actually drove life’s evolution —and it’s the reason behind all of life’s existence. CONSCIOUSNESS, AT THE LEVEL OF THE CELL , cannot produce a human being’s own, complex thoughts, feelings, and sensations; a cell doesn’t have the capacity for abstract thought. But here’s how it does work, says Miller: Imagine a typical situation—daylight in a cell’s environment hits the cell’s external membrane and passes through it. The cell measures that light signal internally, forming a piece of information about the light. “Because it has to analyze it internally, that becomes an experience as the cell analyzes the light to support the state it prefers to be in [to fulfill its function],” Miller says. While that example is of a bacterial cell, all cells absorb various data from their surroundings, analyze them, and make decisions about the actions they should take, such as producing a hormone, or moving in a particular direction, perhaps toward the light.
From early in life’s history, cells of all kinds have combined their skills to further a common goal—to keep on living and reproducing. “Cells have formed colonies. It’s very much like a city that we humans might engineer. It has nutrient channels, an outside and an inside, a collective metabolism,” Miller says. For example, microbes collaborate with each other. They’re codependent, trading resources as well as competing. “In order to make this ecology flourish, each of these cells is taking intelligent action. They’re communicating with one another, and both individually and collectively deploying resources. That’s problem solving and decision making. That’s cognitive action, and it’s one element of consciousness,” he says.
It’s still a hard concept to swallow—that bacteria and other microorganisms are conscious on any level. To animals like us, consciousness is due to a complex nervous system.
.css-2l0eat{font-family:UnitedSans,UnitedSans-roboto,UnitedSans-local,Helvetica,Arial,Sans-serif;font-size:1.625rem;line-height:1.2;margin:0rem;padding:0.9rem 1rem 1rem;}@media(max-width: 48rem){.css-2l0eat{font-size:1.75rem;line-height:1;}}@media(min-width: 48rem){.css-2l0eat{font-size:1.875rem;line-height:1;}}@media(min-width: 64rem){.css-2l0eat{font-size:2.25rem;line-height:1;}}.css-2l0eat b,.css-2l0eat strong{font-family:inherit;font-weight:bold;}.css-2l0eat em,.css-2l0eat i{font-style:italic;font-family:inherit;} “Every aspect of the consciousness that I’m experiencing is a simultaneous aggregation of the consciousnesses of all of my body cells and all of those microbes working in tandem, coordinating so seamlessly that I feel like I’m one individual.”
However, Miller and his fellow authors see this higher, human form of consciousness as a natural property our cells create—together with the more than 10 trillion essential microbes that are a part of our bodies. “Every aspect of the consciousness that I’m experiencing is a simultaneous aggregation of the consciousnesses of all of my body cells and all of those microbes working in tandem, coordinating so seamlessly that I feel like I’m one individual,” he says.
Before exploring that idea further, it’s important to understand one thing: We are holobionts , because we consist of our own host cells and the ones we live with in symbiosis, or mutual cooperation. In particular, we live in symbiosis with a bacterial, viral, and fungal population of cells. In other words, our cells and our microbes mutually benefit one another.
The evolutionary science of the hologenome —that we co-evolved with our microbiome—says that evolution led those first cells to continue forming different kinds of habitats in order to survive and thrive; hence, the development of plants, animals, and fungi. “We’re a constellation of habitats,” says Miller, who spent decades studying the human microbiome and has written several books on the hologenome . He compares human bodies to a successful engineering project for ever more complex groupings of diverse cells living together and adapting to changing environments over millions of years. A form of cellular consciousness has been with us since life first emerged, 3.5 billion years ago. They were able to multiply into abundant varieties of bacteria, amoeba, and then more complex organisms because of their particular awareness. Today, your brain, microbiome and the cells of your gut work together as a community of cells to create your sense of consciousness.
“We are a rich, wonderful, delightful environment for cells,” he says. “So, we bear a resemblance to the first biofilm [microbial colony]. …We are one end result, along with every other creature that can be seen—we are a particular solution to a set of biological cellular problems.”
The authors of The Sentient Cell aren’t alone in hypothesizing that our microbes, the bacteria and viruses in us, have a great deal to do with our consciousness. Various studies show that our own cells communicate with our microbiome, and that our brain, gut, and microbiome are deeply entangled, forming a complex system. Besides being responsible for our health, these complex interactions contribute to our higher level consciousness, according to a 2020 paper in the peer-reviewed Inquiries Journal .
HOWEVER, NOT ALL SCIENTISTS who study the biology of life are convinced that cells are conscious. Cells respond to both chemical and physical signals, including pressure from surrounding cells. The cells of a developing embryo know, for example, when their number has grown to 400. At this exact point, the group begins to separate into three axes that determine the body’s final orientation: front and back, left and right, up and down. They know how to differentiate themselves into the tissues that will become your organs and other parts. Cells are the architects of the organism, cell biologist Alfonso Martínez Arias, Ph.D., tells Popular Mechanics .
His work shows that a person’s genome is a toolbox for the cell to use as it may. Yet we cannot presume that a cell’s behavior is due to consciousness, says Martínez Arias, who spent 40 years at the University of Cambridge researching how a fertilized egg can become an individual with billions of specialized cells.
While cells exhibit behaviors that you could call a sort of intelligence—responding to other cells and their environment—the crux of the problem is that it’s hard to define consciousness, he says. “With cells, there is some kind of computation going on, with an output that can be predicted. …I think increasingly, there is evidence that cells have capacities that are not encoded in the genome.” For instance, the ability to pick and choose from the toolbox of genes that give us our ultimate characteristics. Through experiments, researchers have been able to study cell responses to different chemical and physical stimuli, such as exposing them to a chemical compound that would cause the cells to produce a different compound. “So we are able to communicate with them, but we do it badly. …But I think we are learning their alphabet, we’re learning their language,” Martínez Arias says. He hopes that continuing such investigations will lead us someday to knowing what makes cells tick.
Conventional resistance to labeling cells as “conscious” comes from defining consciousness from a human point of view, Miller believes. We compare our own consciousness to the capacity of other animals, such as the mosquito or the lion. “And the more you look, the more you realize that our form of consciousness, with its own intelligence, is different from other animals, [so our view is skewed].” A cell’s consciousness is more elemental, a simpler form of cognition, he says.
Here’s a practical reason to treat cells as conscious, Miller says: Once we realize that cells are “creative and intelligent problem-solving materials,” we can treat them as partners in designing better biomedical therapies and solutions. By studying their motivations and decision-making, we’ll find more ways to manipulate cells, such as interrupting their processes. For example, cancer cells communicate with each other and with non-cancer cells in the body. We are finding promising cures for some cancers that break down the communication cancer cells use in their efforts to propagate and form tumors. This type of directed immunotherapy leaves patients’ own healthy cells undamaged, unlike chemotherapy, or radiation, which damages healthy cells too.
We’re already taking advantage of cell behavior to engineer microbes that eat plastic. Such creative solutions in the future won’t be possible if we treat cells as robots without preferences, Miller says. We’ll even understand how to explore space better. For example, the radiation levels on a journey to Mars are too high to survive. One of the solutions could be figuring out a way to strengthen our cells against dangerous radiation. Miller believes a study of how cells themselves could engineer an adaptation to radiation would help.
Before joining Popular Mechanics , Manasee Wagh worked as a newspaper reporter, a science journalist, a tech writer, and a computer engineer. She’s always looking for ways to combine the three greatest joys in her life: science, travel, and food.
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By SciTechDaily June 17, 2024
Recent research has produced detailed genomes of sex chromosomes for six ape species, showing significant variability and evolution on the Y chromosome. This work aids in understanding reproductive genetics and could impact studies of human diseases linked to these chromosomes. Credit: SciTechDaily.com
New end-to-end X and Y chromosome sequences uncover enormous variation on the Y chromosome, informing human evolution and disease as well as conservation genetics of endangered apes.
A collaborative research team has generated complete reference genomes for the sex chromosomes of several great and lesser apes, revealing rapid evolutionary changes, particularly on the Y chromosome. These findings provide a basis for future studies on ape reproduction, fertility, and sex-specific genetic traits, enhancing understanding of primate evolution and related human diseases.
An international team from Penn State, the National Human Genome Research Institute, and the University of Washington has produced complete “end-to-end” reference genomes for the sex chromosomes of five great ape species and one lesser ape species. Their research reveals rapid evolutionary changes in the male-specific Y chromosome. These insights enhance our understanding of sex chromosome evolution and contribute to the knowledge of genetic diseases affecting both apes and humans.
“The Y chromosome is important for human fertility, and the X chromosome harbors genes critical for reproduction, cognition, and immunity,” said Kateryna Makova, Verne M. Willaman Chair of Life Sciences, professor of biology at Penn State and leader of the research team. “Our study opens doors for many future investigations of sex chromosomes, how they evolved and diseases associated with them. The living non-human great ape species we studied are all endangered. The availability of their complete sex chromosome sequences will facilitate studies of their sex-specific dispersal in the wild and of their genes important for reproduction and fertility.”
Newly generated, complete genomes for the sex chromosomes of six primate species — produced by an international collaboration led by researchers at Penn State and the National Human Genome Research Institute — reveal rapid evolution on the Y chromosome among apes. These results may inform conservation of these endangered species and shed light on sex-related genetic diseases in both humans and our closest living relatives. Credit: Design: Bob Harris; Photography: San Diego Zoo and Tulsa Zoo
Such reference genomes act as a representative example that are useful for future studies of these species. The team found that, compared to the X chromosome, the Y chromosome varies greatly across ape species and harbors many species-specific sequences. However, it is still subject to purifying natural selection — an evolutionary force that protects its genetic information by removing harmful mutations.
The new study was recently published in the journal Nature .
“Researchers sequenced the human genome in 2001, but it wasn’t actually complete,” Makova said. “The technology available at the time meant that certain gaps weren’t filled in until a renewed effort led by the Telomere-to-Telomere, or T2T, Consortium in 2022-23. We leveraged the experimental and computational methods developed by the Human T2T Consortium to determine the complete sequences for the sex chromosomes of our closest living relatives—great apes.”
The team produced complete sex chromosome sequences for five species of great apes — chimpanzee, bonobo, gorilla, Bornean orangutan and Sumatran orangutan, which comprise most great ape species living today — as well as a lesser ape, siamang. They generated sequences for one individual of each species. The resulting reference genomes act as a map of genes and other chromosomal regions, which can help researchers sequence and assemble the genomes of other individuals of that species. Previous sex chromosome sequences for these species were incomplete or — for the Bornean orangutan and siamang — did not exist.
“The Y chromosome has been challenging to sequence because it contains many repetitive regions, and, because traditional short-read sequencing technology decodes sequences in short bursts, it is difficult to put the resulting segments in the correct order,” said Karol Pál, postdoctoral researcher at Penn State and a co-first author of the study. “T2T methods use long-read sequencing technologies that overcome this challenge. Combined with advances in computational analysis, on which we collaborated with Adam Phillippy’s group at the NHGRI, this allowed us to completely resolve repetitive regions that were previously difficult to sequence and assemble. By comparing the X and Y chromosomes to each other and among species, including to the previously generated human T2T sequences of the X and the Y, we learned many new things about their evolution.”
“Sex chromosomes started like any other chromosome pair, but the Y has been unique in accumulating many deletions, other mutations and repetitive elements because it does not exchange genetic information with other chromosomes over most of its length,” said Makova, who is also the director of the Center for Medical Genomics at Penn State.
As a result, across the six ape species, the research team found that the Y chromosome was much more variable than the X over a variety of characteristics, including size. Among the studied apes, the X chromosome ranges in size from 154 million letters of the ACTG alphabet — representing the nucleotides that make up DNA — in chimpanzee and human to 178 million letters in gorilla. In contrast, the Y chromosome ranges from 30 million DNA letters in siamang to 68 million letters in Sumatran orangutan.
The amount of DNA sequence shared between species was also more variable on the Y. For example, about 98% of the X chromosome aligns between human and chimpanzee, but only about a third of the Y aligns between them. The researchers found that this is in part because the Y chromosome is more likely to be rearranged or have portions of its genetic material duplicated.
Additionally, the percentage of the chromosome occupied by sequences that are repeated is highly variable on the Y. Whereas, depending on the species, 62% to 66% of the X chromosomes are occupied by repetitive elements, 71% to 85% of the Y chromosomes are occupied by them. These percentages are higher on both the X and the Y than in other chromosomes in the human genome.
“We found the ape Y to be shrinking, accumulating many mutations and repeats, and losing genes,” Makova said. “So why hasn’t the Y chromosome disappeared, as some previous hypotheses suggested? In collaboration with Sergei Kosakovsky Pond from Temple University and others, we found that the Y chromosome still has a number of genes evolving under purifying selection — a type of natural selection that keeps gene sequences intact. Many of these genes are important for spermatogenesis. This means that the Y chromosome is unlikely to disappear any time soon.”
The researchers found that many genes on the Y chromosome seem to use two strategies to survive. The first takes advantage of genetic redundancy — the presence of multiple copies of the same gene on a chromosome — so that intact copies of the gene can compensate for copies that might acquire mutations. The team quantified this genetic redundancy by completing the landscape of multi-copy gene families on ape sex chromosomes for the first time.
The second survival strategy takes advantage of palindromes, where the sequence of letters in the DNA alphabet is followed by the same, but inverted sequence, for example, ACTG-GTCA. When located within a palindrome, genes benefit from the palindrome’s ability to correct mutations.
“We found that the Y chromosome can exchange genetic information with itself between the repeated sequences of the two palindrome arms, which fold so that the inverted sequences align,” Pál said. “When two copies of the same gene are located within palindromes, and one copy is hit by a mutation, the mutation can be rescued by the genetic exchange with another copy. This can compensate for the Y’s lack of genetic information exchange with the other chromosomes.”
The research team obtained the complete sequences of palindromes on ape sex chromosomes also for the first time, as they were previously difficult to sequence and study. They found that palindromes are particularly abundant and long on the ape Y chromosome, yet they are usually only shared among closely related species.
In collaboration with Michael Schatz and his team at Johns Hopkins University, the researchers also studied the sex chromosomes of 129 individual gorillas and chimpanzees to better understand the genetic variation within each species and search for evidence of natural selection and other evolutionary forces acting on them.
“We obtained substantial new information from previously studied gorilla and chimpanzee individuals by aligning their sex chromosome sequencing reads to our new reference sequences,” said Zachary Szpiech, assistant professor of biology at Penn State and an author of the paper. “While increasing the sample size in the future will be very helpful to improve our ability to detect signatures of different evolutionary forces, this can be ethically and logistically challenging when working with endangered species, so it is critical that we can get the most out of the data we do have.”
The researchers explored a variety of factors that could explain variation on the Y chromosome within gorillas and within chimpanzees, and this analysis revealed additional signatures of purifying selection on the Y. This confirms the role of this type of natural selection on the Y, as was discovered in their previous analyses of genes.
“The powerful combination of bioinformatic techniques and evolutionary analyses that we used allows us to better explain the evolutionary processes acting on sex chromosomes in our closest living relatives, great apes,” said Christian Huber, assistant professor of biology at Penn State and an author of the paper. “Additionally, the reference genomes we produced will be instrumental for future studies of primate evolution and human diseases.”
For more on this research, see Evolutionary Insights Revealed by First Complete Chromosome Sequences From Great Apes .
Reference: “The complete sequence and comparative analysis of ape sex chromosomes” by Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris, Gabrielle A. Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C. McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G. Bouffard, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E. Cook, Sarah J. C. Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage H. Garcia, Patrick G. S. Grady, Richard E. Green, Diana Haddad, Pille Hallast, William T. Harvey, Glenn Hickey, David A. Hillis, Savannah J. Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L. Kosakovsky Pond, Troy M. LaPolice, Charles Lee, Alexandra P. Lewis, Yong-Hwee E. Loh, Patrick Masterson, Kelly M. McGarvey, Rajiv C. McCoy, Paul Medvedev, Karen H. Miga, Katherine M. Munson, Evgenia Pak, Benedict Paten, Brendan J. Pinto, Tamara Potapova, Arang Rhie, Joana L. Rocha, Fedor Ryabov, Oliver A. Ryder, Samuel Sacco, Kishwar Shafin, Valery A. Shepelev, Viviane Slon, Steven J. Solar, Jessica M. Storer, Peter H. Sudmant, Sweetalana, Alex Sweeten, Michael G. Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A. Wilson, Alice C. Young, Huiqing Zeng, Xinru Zhang, Zachary A. Szpiech, Christian D. Huber, Jennifer L. Gerton, Soojin V. Yi, Michael C. Schatz, Ivan A. Alexandrov, Sergey Koren, Rachel J. O’Neill, Evan E. Eichler and Adam M. Phillippy, 29 May 2024, Nature . DOI: 10.1038/s41586-024-07473-2
In addition to Makova, Pál, Szpiech and Huber, the research team at Penn State includes Kaivan Kamali, computational scientist in the departments of biology and of biochemistry and molecular biology; Troy LaPolice, graduate student in bioinformatics and genomics; Paul Medvedev, professor of computer science and engineering and of biochemistry and molecular biology; Sweetalana, research assistant in the department of biology; Huiqing Zeng, research technologist in biology; Xinru Zhang, graduate student in bioinformatics and genomics; Robert Harris, assistant research professor of biology, now retired; Barbara McGrath, associate research professor of biology, now retired; and Sarah Craig, associate research professor of biology, currently a program officer at the National Institutes of Health . The co-authors also included Penn State alumni Monika Cechova, currently a postdoctoral fellow at the University of California Santa Cruz, and Melissa Wilson, currently an associate professor at Arizona State University.
In addition to Makova, the team was co-led by co-corresponding study authors Adam Phillippy, senior investigator at NHGRI, and Evan Eichler, professor of Genome Sciences at the University of Washington.
Funding from the National Institutes of Health supported this research.
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Evolution may be purposeful and it’s freaking scientists out.
scientists are worried
“Where are all the genetic cures?” asks Denis Noble, a frustrated biophysicist, Royal Society fellow and pioneer of the field of systems biology. “They don’t exist. Where will they be? They won’t exist.” Since mapping the human genome in 2003, research priorities and funding shifted significantly towards genetics. The investment improved disease detection and management but failed to deliver on its promise of cures for our most common deadly diseases like heart disease, type 2 diabetes, Alzheimer’s and most cancers. Compounding the issue, a large-scale, 2023 study concluded that genetic risk scores perform poorly at predicting who’s going to develop common diseases. For Noble, the billions invested annually in genetic research represents less of a strategy and more of a scientific confusion—that we are our genes.
The scientific story of who we are is a reductionist, gene-centric model that forfeits natural phenomena like purpose due to its association with intelligent design and a transcendent, intelligent designer. Noble is neutral on religious matters. Yet he sees compelling evidence that purpose may be fundamental to life. He’s determined to debunk the current scientific paradigm and replace the elevated importance of genes with something much more controversial. His efforts have enraged many of his peers but gained support from the next generation of origins-of-life researchers working to topple the reign of gene-centrism. If successful, the shift could not only transform how we classify, study and treat disease, but what it means to be alive.
One of the earliest biomedical computer programmers, Noble created the first model for a working human heart in 1960 on a vacuum tube computer. The project led to his discovery that heartbeats are emergent properties—new phenomena—arising from feedback loops, transforming our understanding of heart function and underpin treatments for heart conditions that we use today. His research on the heart’s pacemaker demonstrates a prioritization of the organism as a whole over its genes alone. “Several genes could individually be knocked out but the process continues,” says Noble. These genes are responsible for heart rhythm, yet other mechanisms can take over to get the job done.
In the 1960s, Noble served as the dissertation examiner for the then-unknown Richard Dawkins. Dawkins—a prominent figure in the New Atheism movement—would go on to author the 1976 classic The Selfish Gene that popularized the gene-centric theory of evolution. Gene-centrism says evolution acts on genes, not individual organisms. We are merely vessels for our genes that are driving evolution by Darwinian natural selection. Noble's analysis suggests that evolution acts on the organism as a whole, with the organism harnessing randomness and variation to create and heal itself—on purpose. In this re-evaluation, Noble believes that purpose, creativity, and innovation are fundamental to evolution. He argues that we experience these processes as drives, but they are not purely subjective. They also progress non-consciously in other parts of our body. These natural processes harness randomness and unpredictability—stochasticity—to survive, make decisions, and thrive. “Stochasticity is the center of creativity in organisms,” says Noble.
Noble’s formal training is in cellular electrophysiology, the study of the differences in electrical charges inside and outside of a cell membrane. He suspects that crevices of ancient rocks served as cradles for emergent self-sustaining systems. Eventually, membranes evolved from lipid-coated bubbles, replacing the fissures in rocks as containers for these emergent systems. This gave rise to the first living entity—a single-celled organism. According to Noble, the constraints of a cell’s membrane and the restriction of freedom of molecules inside a cell, made purpose both possible and necessary. This development required a sort of intention or cognition within emergent networks of molecules to create and sustain biological functions.
Best 5% interest savings accounts of 2024, reinterpreting existing evidence.
Noble sees evidence of purposive and intentional evolution in our immune response to viruses. Detection of the invader triggers a flurry of rapid mutations in the genes of B cells, creating a legion of gene variants. These variants are antibodies, the most effective of which are deployed to combat the virus. In a defensive assault, the immune system self-modifies its own DNA. “It changes the genome. Not supposed to be possible,” says Noble. “Happens all the time.”
The conventional view is that this is still random natural selection—cranked up to warp speed inside the body during the lifetime of an individual organism. Noble agrees, but adds the observation that the organism’s immune system initiates and orchestrates the ramped up process, harnessing natural selection to fight off the invader. For Noble, this routine procedure offers clear evidence of the organism actively participating in its own evolution—it’s doing natural selection. This is an alternative theory of evolution where cognition is fundamental. In this theory, the smallest unit of life—cells—have some version of intelligence and intent that allows them to detect and respond to their environment. Noble clocks the immune response as a goal-directed pattern of behavior at the cellular level that scales to every level of organization within a living system. He believes we’re working ourselves into a sweat to exclude something so essential to evolution and to life as purpose and intention.
Noble is part of The Third Way, a movement in evolutionary biology that views natural selection as part of a holistic, organism-centered process. He co-authored Evolution “on Purpose," published by MIT Press in 2023, which argues that organisms evolve with intention.
Recent research calls into question whether genetic mutations are even entirely random. A 2022 study in Nature shows a mutation bias supporting the organism as a whole. Noble doesn’t understand why studies like these aren’t making bigger waves. “Do you, you people working in gene-centric biology, do you realize what has already been published?” asks an incredulous Noble.
This is one of his central criticisms of Richard Dawkins, whom Noble dubs the primary exponent of gene-centrism. Dawkins is one of the world’s foremost science communicators. Noble considers Dawkins an exceptional writer who simply hasn’t kept up with the science. When asked for comment, Dawkins responded, “I have a whole chapter dealing with Denis Noble in my next book, The Genetic Book of the Dead . It will be available in September.”
Noble attributes our legacy of missteps to rigid assumptions put in place over a century ago to stand in for a lack of evidence. Darwin’s namesake theory of evolution by natural selection was first published in 1859. This slow process alters instructions to build an organism only through genetic mechanisms like random mutations and recombination that get passed down to offspring.
Near the end of his life, Darwin was corresponding with physiologist George Romanes, exploring additional mechanisms of inheritance and the role of physiology. Despite Darwin’s broadening views, his theory was scaled back posthumously. Following Darwin’s death in 1882, biologist and ‘Neo-Darwinist’ August Weismann promulgated the idea of a one-way barrier cordoning off reproductive cells from the rest of the body. This barrier required that reproductive cells were the sole vehicles for inheritance. Neo-Darwinists would go on to revive a theory of genes and genetic recombination. Mendelian genetics with Darwin’s natural selection were synthesized. The reproductive cells became the housing for genes which ascended to the centerpiece for evolution.
In 1894 at age 46, Romanes died of a cerebral hemorrhage. And so died the lone voice advocating for Darwin’s ultimate views—views of evolution which emphasized more complexity and physiology. Noble suspects if Romanes had survived, we may have avoided a gene-centric paradigm paralysis. Instead, Noble feels “our genetic hope is more about faith than facts.”
Noble is urgently reviving and expanding on Darwin and Romanes. Last month, a special edition of The Journal of Physiology, co-edited by Noble and Michael Joyner of the Mayo Clinic, featured 21 articles challenging current evolutionary theory and advocating for the inclusion of phenomena like agency and cognition.
These articles corroborate the general theme that Genes Are Not The Blueprint For Life , the title of Noble’s review in the journal Nature, heralding science writer Philip Ball’s primer How Life Works: A User’s Guide to The New Biology. Ball, a former editor of Nature, admonishes the life sciences for ignoring obvious natural properties of living systems like agency and purpose because of “quasi-mystical” associations with intelligent design. In the book, Ball illustrates the resistance to letting go of the “tidy tale” of gene-centrism and the idea that genes control health more than “‘a bit’ and ‘somewhat’.” Like Noble, Ball is advocating for a new biology.
Noble’s urgency is more than academic. “This is critical to the future of health care,” says Noble, who feels the public is paying the ultimate price for gene-centrism. “I face the same problem as many other people face,” says Noble. “Families having to deal with serious illness, with social care that costs more than you can ever afford. I've been through all of that. I know what it does to families.” He considers it a foregone conclusion that aging populations will strain health systems to the point of rupture if we continue with gene-centrism.
Noble’s critics worry that entertaining religion-adjacent views subverts established science and the entire scientific project. But Noble’s research doesn’t challenge the scientific method. It challenges a scientific epoch marked by a purely mechanistic view of nature that coincided with the Industrial Revolution and age of mechanization. Noble appreciates concerns raised by skeptics, yet refuses to exclude natural phenomena from scientific inquiry.
Noble’s critics also accuse him of exaggerating the importance of physiology, while Noble insists physiology has been unjustly sidelined since Darwin. “Physiology now has to come to the rescue of evolutionary biology,” says Noble.
Another objection is that Noble is contesting a theory of evolution that has since been revised to address new evidence. For Noble, this is exactly his point. New evidence doesn’t merely refine the theory, it undermines it.
Biology’s existential crisis reached a flashpoint in 2016, when Noble and a group of scientists and philosophers organized a conference on New Trends in Evolutionary Biology with the Royal Society of London. Royal Society members petitioned—unsuccessfully—to kill it. The protest letter (Royal Society member Richard Dawkins’ signature was noticeably absent) read “...we wish to express our concern that this meeting will severely damage the reputation of the Society among the worldwide community of evolutionary biologists (it has already attracted adverse comments among colleagues in the USA).”
They never name their U.S. colleagues, although American biologist and prominent anti-creationist, Jerry Coyne uses words like "stupid," "rotten" and “blundering tyro” in his public condemnation of Noble. Canadian biologist Laurence A. Moran echoes Coyne’s outrage adding, “It's difficult not to be very angry at people like Denis Noble.” Moran writes that if science was working properly, Noble would “fade into the woodwork of the Senior Common Room at some college in Oxford.” It’s true Noble didn’t raise serious objections to evolutionary theory until after he retired as Chair of Cardiovascular Physiology at the University of Oxford in 2004. He says “coming out” would have invariably damaged the reputation and careers of the research team in his lab.
“We need to shame them. I'm sorry, but we do,” says bioengineer and origins-of-life scientist Joana Xavier about Noble’s caustic critics. Xavier, a next-generation evolutionary theorist, resents “bullying” from prominent scientists that shuts down young biologists and stymies scientific progress. She and her peers have new tools and fresh perspectives, yet Xavier says their academic careers are jeopardized by demeaning attacks.
Xavier’s research made headlines for her discovery of emergent, cooperative networks of molecules that mutually catalyze each other's formation in ancient bacteria. These systems were first theorized by complexity scientist, Stuart Kauffman, as a candidate for the origins-of-life story that challenges gene-centrism. Xavier studied under Noble and Kauffman before launching the Origin of Life Early-Career Network (OoLEN) with over 200 young, interdisciplinary researchers from around the world. This group co-authored an inaugural scientific paper The Future of Origin of Life Research: Bridging Decades-Old Divisions.
Xavier has identified another indication of intention at the cellular level of emergent systems: cooperation . She doesn’t understand why it’s acceptable to think of evolution as competitive but evidence of cooperation is considered taboo. “I think to solve life's origins, we'll need to look much more at cooperation. And emergence really brings cooperation into the scene, whether you want it or not,” says Xavier, who also sees creativity as fundamental to life. “It's so obvious, you either accept that it is true that life is creative or you don't.”
Xavier says her field is at an inflection point with gene-centrism holding back progress in health and medicine. “I think we’re completely stuck,” says Xavier. She’s actively pushing in a new direction even if she has to leave academia for the private sector to do it. “The gene-centric paradigm,” says Xavier, “That has to go. It's urgent.”
These days, Noble is surrounded by young researchers eager to reopen the case of evolution. “I have young people helping me with all of this because, believe me, I can't do all of this on my own,” says Noble. Creativity, purpose and organism-centered evolution are still only postulates that need rigorous testing. Noble is eager to explore both his theory and others. With theories of who we are, how we heal, and how we came to exist, Noble stresses “we should have more than one horse in the race.”
Watch the interviews with Noble and others that informed this article here:
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Using a combination of machine learning and playback experiments in the field, we find that African savannah elephants address members of their family with individually specific, name-like calls. These ‘names’ are probably not imitative of the receiver’s calls, which is similar to human naming but unlike known phenomena in other animals.
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