The Science of Solidarity

By: Alexandria Addesso

To many Charles Darwin is the utmost authority when it comes to the study of evolution. Many people took his findings about the importance of competition and how it plays a role in evolution and ran with it. Even as far as applying it to society and thus creating social Darwinism. Anarcho-scientist Peter Kropotkin was inspired by the publication of On the Origin of Species to go and do his own observations of a multitude of species and seemed to come to the opposite conclusion of such Darwinism backers. He argued against claims that competition alone led to evolution or ‘survival of the fittest’, and insisted that mutual aid is a major factor of evolution. The following is an introductory excerpt from Kropotkin’s book Mutual Aid: A Factor of Evolution.

Two aspects of animal life impressed me most during the journeys which I made in my youth in Eastern Siberia and Northern Manchuria. One of them was the extreme severity of the struggle for existence which most species of animals have to carry on against an inclement Nature; the enormous destruction of life which periodically results from natural agencies; and the consequent paucity of life over the vast territory which fell under my observation. And the other was, that even in those few spots where animal life teemed in abundance, I failed to find – although I was eagerly looking for it – that bitter struggle for the means of existence, among animals belonging to the same species, which was considered by most Darwinists (though not always by Darwin himself) as the dominant characteristic of struggle for life, and the main factor of evolution.



Kropotkin chronicled his findings while observing a wide variety of insects, birds, sea-life, and different mammals including humans. When it came to who was fittest to survive and further their species, it was most often those who cooperated via forms of mutual aid and solidarity.

As soon as we study animals – not in laboratories and museums only, but in the forest and the prairie, in the steppe and the mountains – we at once perceive that though there is an immense amount of warfare and extermination going on amidst various species, and especially amidst various classes of animals, there is, at the same time, as much, or perhaps even more, of mutual support, mutual aid, and mutual defense amidst animals belonging to the same species or, at least, to the same society. Sociability is as much a law of nature as mutual struggle. Of course it would be extremely difficult to estimate, however roughly, the relative numerical importance of both these series of facts. But if we resort to an indirect test, and ask Nature: "Who are the fittest: those who are continually at war with each other, or those who support one another?" we at once see that those animals which acquire habits of mutual aid are undoubtedly the fittest. They have more chances to survive, and they attain, in their respective classes, the highest development of intelligence and bodily organization. If the numberless facts which can be brought forward to support this view are taken into account, we may safely say that mutual aid is as much a law of animal life as mutual struggle, but that, as a factor of evolution, it most probably has a far greater importance, inasmuch as it favours the development of such habits and characters as insure the maintenance and further development of the species, together with the greatest amount of welfare and enjoyment of life for the individual, with the least waste of energy.



Solidarity scientifically leads to the continuation of life. Through the solidarity of family units, as wells even sometimes larger communities, children are able to be raised and protected. Solidarity is also pivotal for any revolution, social movement, or major change to occur. The slogan “workers of the world unite,” first mentioned in the Communist Manifesto in 1848, called for solidarity among all proletariat (the lower/working class) regardless to nation or ethnicity. These were truly powerful words of unity for those across a particular class line against their oppressors that belonged to the bourgeoisie (the middle/capitalist class).

A major group that unified lower class people across ethnic and gender lines on U.S. soil in the aftermath of the Democratic Convention protests of 1968 was the original Rainbow Coalition. It was formed by the Illinois Chapter of The Black Panthers in Chicago and also included the Young Patriots (a group of white youth who had migrated from Appalachia to Chicago), the Young Lords (a group of Puerto Rican nationalist youth), disenfranchised jewish youth and members of the women’s movement. The Rainbow Coalition epitomized solidarity and intersectionality within the class struggle. Because of its diversity, the Rainbow Coalition was able to bring about treaties among violent rivaling gangs as well as fight against police brutality that did nothing but add to the wave of violence. With unity comes power, and this was highly threatening to both local and national government.



“It seems to me that a lot of the real intense government repression didn’t happen until the Black Panthers started building coalitions,” said Bobby Lee a Black Panthers member who helped organize the Rainbow Coalition along with Deputy Chairman of the Illinois Chapter Fred Hampton, in an interview with Chicago Area. “Once the party departed from the ‘hate whitey’ trip and got serious about building real politics, we were a threat—plain and simple. The FBI were always watching us. But the Rainbow Coalition was their worst nightmare.”

For major changes to occur, for the preservation of life, and to strive towards survival and thus evolution, solidarity is a major factor.

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The Evolution of Area 51

By: Alexandria Addesso

Area 51 has seemed to exist in two different places for decades, on both the southern shore of Groom Lake about 83 miles north-west of Las Vegas, and in the collective consciousness of those who can only imagine the whereabouts of the military base that has long been kept “top secret” and confidential. Over three-dozen films have been made about Area 51 as well as a host of mini-series despite the fact that very little information about the base has been verified. The idea of Area 51 has definitely evolved over the years.

Area 51 was built in 1941 and was given the official name of “Watertown” in 1956. Other monikers for the test site were Paradise Ranch and Dreamland, the latter was based on a poem by Edgar Allen Poe. The site was originally used as an auxiliary airfield. By 1951 the base was being utilized by the Central Intelligence Agency (CIA) to develop the Lockheed U-2 reconnaissance aircraft, an American single-jet engine, ultra-high altitude aircraft nicknamed “The Dragon Lady.” It is believed that over half of the unidentified flying object (UFO) sightings during the 1950s and 1960s were actually U-2 aircrafts.



This of course has helped contribute to the largely believed lure that aliens as well as their spacecrafts have been or are currently held at Area 51. It is true that aside from the U-2, numerous odd looking aircrafts have been developed, held and tested at the base. Most of which are used for spying or other military purposes. Also many of the projects done at the site are deemed confidential, to which information and details of can never be disclosed. Despite this fact many so called past employees of the base have “leaked” information. Retired Area 51 scientist Boyd Bushman released a video in which he describes the base as containing aliens, UFOs, and anti-gravity projects. The video was released right before his death.



Whether or not you believe that the confidential information about what is done at Area 51 has to do with alien life forms or not seems to be influence on your belief in extraterrestrials in general. Top secret projects done at the base having to do with both domestic and international spying is already factually known. Another reason why certain projects at Area 51 are kept confidential is because they can actually harm the general population. In the 1970s and 1980s Area 51 employees were repeatedly exposed to jet fuel toxins. In 1996 Helen Frost, the wife of one of the employees that died from these toxins, brought up a lawsuit against the United States government but it was dismissed because such allegations could not be “confirmed” and the base is exempt from any environmental laws.

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Are we closer than ever to a timeline for human evolution?

Dating when our ancestors split from Neanderthals and other relatives has long been a puzzle, but DNA advances are making our evolutionaNeanderthalsy journey clearer

Anthropologists and geneticists had a problem. And the farther back in time they looked, the bigger the problem became.

For the past several years, there have been two main genetic methods to date evolutionary divergences - when our ancestors split from Neanderthals, chimpanzees, and other relatives. The problem was, the results of these methods differed by nearly two-fold.

By one estimate, modern humans split from Neanderthals roughly 300,000 years ago. By the other, the split was closer to 600,000 years ago. Likewise, modern humans and chimps may have diverged around 6.5 or 13 million years ago.

Puzzled by this wild disagreement, researchers with diverse expertise have been studying it from different angles. Their combined discoveries, recently reviewed, here, have shed light on how genetic differences accumulate over time and have advanced methods of genetic dating.



And if you’re in suspense, yes, they’ve also pinned down important events in our evolutionary timeline. Everyone alive today seems to share ancestors with each other just over 200,000 years ago and with Neanderthals between 765,000-550,000 years ago.

Dating with the molecular clock
Go back in time and you’ll find a population of Homo sapiens who were the ancestors of everyone living today. Go back farther and our lineage meets up with Neanderthals, then chimps, and eventually all primates, mammals, and life.
In order to date these evolutionary splits, geneticists have relied on the molecular clock - the idea that genetic mutations accumulate at a steady rate over time. Specifically this, concerns mutations that become neutral substitutions, or lasting changes to letters of the genetic code that do not affect an organism’s chances of surviving and reproducing.



If such mutations arise clocklike, then calculating the time since two organisms shared common ancestors should be as easy as dividing the number of genetic differences between them by the mutation rate - the same way that dividing distance by speed gives you travel time.

But you need to know the rate.
For decades, anthropologists used fossil calibration to generate the so-called phylogenetic rate (a phylogeny is a tree showing evolutionary relationships). They took the geologic age of fossils from evolutionary branch points and calculated how fast mutations must have arisen along the resulting lineages.

For example, the earliest fossils on the human branch after our split with chimps are identified by the fact that they seem to have walked on two legs; bipedalism is
the first obvious difference that distinguishes our evolutionary lineage of hominins from that of chimps. These fossils are 7-6 million years old, and therefore the chimp-human split should be around that age. Dividing the number of genetic differences between living chimps and humans by 6.5 million years provides a mutation rate.

Determined this way, the mutation rate is 0.000000001 (or 1x10-9) mutations per DNA base pair per year. Applied to genomes with 6 billion base pairs, that means over millions of years of chimp and human evolution, and there have been on average six changes to letters of the genetic code per year.

Why archaeology needs to come out of the cave and into the digital age
This rate can be used to date evolutionary events that are not evident from fossils, such as the spread of modern humans out of Africa.



But genetic dating got messy in 2010, when improvements to DNA sequencing allowed researchers to determine the number of genetic differences between parents and their children. Known as pedigree analysis, this provides a more direct measurement of the current mutation rate within one generation, rather than an average over millions of years.

Pedigree analysis counts 60-some mutations every generation; that converts to a rate approximately half the phylogenetic estimate—meaning evolutionary events would be twice as old.

The erratic molecular clock
Resolving this disagreement propelled researchers to reassess and revise their starting assumptions: How accurately were they counting the small number of differences between genomes of parents and children? Were fossils assigned to the correct branches of the evolutionary tree? And above all, how constant is the molecular clock?

It turns out that among primates, the molecular clock varies significantly by species, sex, and mutation type. A recent study found that New World monkeys (i.e. monkeys of the Americas like marmosets and squirrel monkeys) have substitution rates about 64% higher than apes (including humans). Within apes, rates are about 7% higher in gorillas and 2% higher in chimpanzees, compared to humans.



But even among humans, mutation rates differ, particularly between the sexes with age. As fathers get older, they gain about one additional mutation per year in the DNA they can pass on to children. Mothers, on the other hand, accumulate considerably fewer mutations with each passing year.

These species and sex differences make sense when you consider how mutations form. Most heritable mutations occur from mistakes when DNA copies itself in the germline, or cells leading to eggs and sperm. The number of times germline DNA has to copy itself depends on developmental and reproductive variables including age at puberty, age at reproduction, and the process of sperm production.
These traits vary across primates today and certainly varied over primate evolution.

For instance, average generation times are six years for New World monkeys, 19 years for gorillas, 25 years for chimps, and 29 years for humans.

And those extra mutations as fathers get older? Sperm are produced continuously after puberty, so sperm made later in life are the result of more rounds of DNA replication and opportunities for replication errors. In contrast, a mother’s stock of eggs is formed by birth. The small increase with maternal age could be due to mutations from DNA damage, rather than replication errors.

Ways forward for dating backwards
It’s now clear that one mutation rate cannot determine the dates for all divergences relevant to human evolution. However, researchers can secure the timeline for important evolutionary events by combining new methods of genetic dating with fossils and geologic ages.

Innovative computational methods have incorporated reproductive variables into calculations. By taking into account ages of reproduction in both sexes, age of male puberty, and sperm production rates, researchers have estimated split times that accord with the fossil record.



Another new approach has analyzed mutations that are mainly independent of DNA replication. It seems that certain classes of mutations, related to DNA damage, do behave more clocklike.

And some researchers have focused on ancient DNA. Comparing human fossils from the past 50,000 years to humans today, suggests a mutation rate that agrees with pedigree analysis.

At least one evolutionary split was pinned down in 2016, after ancient DNA was extracted from 430,000 year-old hominin fossils from ‘Sima de los Huesos’, Spain. The Sima hominins looked like early members of the Neanderthal lineage based on morphological similarities. This hypothesis fit the timing of the split between Neanderthals and modern humans based on pedigree analysis (765,000-550,000 years ago), but did not work with the phylogenetic estimate (383,000-275,000 years ago).
Where do the Sima hominins belong on our family tree? Were they ancestors of both Neanderthals and modern humans, just Neanderthals, or neither?

DNA answered this definitively. The Sima hominins belong to the Neanderthal branch after it split with modern humans. Moreover, the result provides a firm time point in our family tree, suggesting that the pedigree rate works for this period of human evolution.

Neanderthals and modern humans likely diverged between 765,000-550,000 years ago. Other evolutionary splits may soon be clarified as well, thanks to advances brought about by the mutation rate debates. Someday soon, when you see a chimp, you may be able to salute your great, great… great grandparent, with the correct number of “greats.”
Source: Biology News

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Scientists engineer animals with ancient genes to test causes of evolution

A transgenic fruit fly engineered to carry the alcohol dehydrogenase gene as it existed about 4 million years ago. Thousands of these 'ancestralized' flies were bred and studied for their ability to metabolize alcohol and to survive on an.

Scientists at the University of Chicago have created the first genetically modified animals containing reconstructed ancient genes, which they used to test the evolutionary effects of genetic changes that happened in the deep past on the animals' biology and fitness.

The research, published early online in Nature Ecology & Evolution on Jan. 13, is a major step forward for efforts to study the genetic basis of adaptation and evolution. The specific findings, involving the fruit fly's ability to break down alcohol in rotting fruit, overturn a widely-held hypothesis about the molecular causes of one of evolutionary biology's classic cases of adaptation.



"One of the major goals of modern evolutionary biology is to identify the genes that caused species to adapt to new environments, but it's been hard to do that directly, because we've had no way to test the effects of ancient genes on animal biology," said Mo Siddiq, a graduate student in the Department of Ecology and Evolution at the University of Chicago, one of the study's lead scientists.

"We realized we could overcome this problem by combining two recently developed methods—statistical reconstruction of ancient gene sequences and engineering of transgenic animals," he said.

Until recently, most studies of molecular adaptation have analyzed gene sequences to identify "signatures of selection"—patterns suggesting that a gene changed so quickly during its evolution that selection is likely to have been the cause. The evidence from this approach is only circumstantial, however, because genes can evolve quickly for many reasons, such as chance, fluctuations in population size, or selection for functions unrelated to the environmental conditions to which the organism is thought to have adapted.

Siddiq and his advisor, Joe Thornton, PhD, professor of ecology and evolution and human genetics at the University of Chicago, wanted to directly test the effects of a gene's evolution on adaptation. Thornton has pioneered methods for reconstructing ancestral genes—statistically determining their sequences from large databases of present-day sequences, then synthesizing them and experimentally studying their molecular properties in the laboratory. This strategy has yielded major insights into the mechanisms by which biochemical functions evolve.

Thornton and Siddiq reasoned that by combining ancestral gene reconstruction with techniques for engineering transgenic animals, they could study how genetic changes that occurred in the deep past affected whole organisms-their development, physiology, and even their fitness.



"This strategy of engineering 'ancestralized animals' could be applied to many evolutionary questions," Thornton said. "For the first test case, we chose a classic example of adaptation-how fruit flies evolved the ability to survive the high alcohol concentrations found in rotting fruit. We found that the accepted wisdom about the molecular causes of the flies' evolution is simply wrong."

The fruit fly Drosophila melanogaster is one of the most studied organisms in genetics and evolution. In the wild, D. melanogaster lives in alcohol-rich rotting fruit, tolerating far higher alcohol concentrations than its closest relatives, which live on other food sources. Twenty-five years ago at the University of Chicago, biologists Martin Kreitman and John McDonald invented a new statistical method for finding signatures of selection, which remains to this day one of the most widely used methods in molecular evolution. They demonstrated it on the alcohol dehydrogenase (Adh) gene—the gene for the enzyme that breaks down alcohol inside cells—from this group of flies. Adh had a strong signature of selection, and it was already known that D. melanogaster flies break down alcohol faster than their relatives. So, the idea that the Adh enzyme was the cause of the fruit fly's adaptation to ethanol became the first accepted case of a specific gene that mediated adaptive evolution of a species.

Siddiq and Thornton realized that this hypothesis could be tested directly using the new technologies. Siddiq first inferred the sequences of ancient Adh genes from just before and just after D. melanogaster evolved its ethanol tolerance, some two to four million years ago. He synthesized these genes biochemically, expressed them, and used biochemical methods to measure their ability to break down alcohol in a test tube.



The results were surprising: the genetic changes that occurred during the evolution of D. melanogaster had no detectable effect on the protein's function.
Working with collaborators David Loehlin at the University of Wisconsin and Kristi

Montooth at the University of Nebraska, Siddiq then created and characterized transgenic flies containing the reconstructed ancestral forms of Adh. They bred thousands of these "ancestralized" flies, tested how quickly they could break down alcohol, and how well the larvae and adult flies survived when raised on food with high alcohol content. Surprisingly, the transgenic flies carrying the more recent Adh were no better at metabolizing alcohol than flies carrying the more ancient form of Adh. Even more strikingly, they were no better able to grow or survive on increasing alcohol concentrations. Thus, none of the predictions of the classic version of the story were fulfilled. There is no doubt that D. melanogaster did adapt to high-alcohol food sources during its evolution, but not because of changes in the Adh enzyme.

"The Adh story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction. But three lines of circumstantial evidence don't make an airtight case," Thornton said. "That's why we wanted to test the hypothesis directly, now that we finally have the means to do so."

Siddiq and Thornton hope that the strategy of making ancestralized transgenic will become the gold standard in the field to decisively determine the historical changes in genes to their changes on organisms' biology and fitness.

For his part, Kreitman, who is still a professor of ecology and evolution at UChicago, has been supportive of the new research, helping advise Siddiq on the project and sharing his vast knowledge about molecular evolution and Drosophila genetics.



"From the beginning, Marty was excited about our experiments, and he was just as supportive when our results overturned well-known conclusions based on his past work," Siddiq said. "I think that's extremely inspiring."

Source: University of Chicago, Medical Center

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Amazing Discovery: Viruses are Dominant Drivers of Human Evolution, Researchers Say

In a new study, scientists apply big-data analysis to reveal the full extent of viruses’ impact on the evolution of humans and other mammals. Their findings suggest 30% of all protein adaptations since humans’ divergence with chimpanzees have been driven by viruses.

When an environmental change occurs, species are able to adapt in response due to mutations in their DNA. Although these mutations occur randomly, by chance some of them make the organism better suited to their new environment. These are known as adaptive mutations.

In the past decade, scientists have discovered a large number of adaptive mutations in a wide variety of locations in the genome of humans and other mammals.



The fact that adaptive mutations are so pervasive is puzzling. What kind of environmental pressure could possibly drive so much adaptation in so many parts of the genome?

Viruses are ideal suspects since they are always present, ever-changing and interact with hundreds to thousands of proteins.

“When you have a pandemic or an epidemic at some point in evolution, the population that is targeted by the virus either adapts, or goes extinct,” said lead author Dr. David Enard, of Stanford University.

“We knew that, but what really surprised us is the strength and clarity of the pattern we found.”

Previous research on the interactions between viruses and proteins has focused on individual proteins that are directly involved in the immune response.

This is the first study to take a global look at all types of proteins.

“The big advancement here is that it’s not only very specialized immune proteins that adapt against viruses,” Dr. Enard said.

“Pretty much any type of protein that comes into contact with viruses can participate in the adaptation against viruses. It turns out that there is at least as much adaptation outside of the immune response as within it.”



The team’s first step was to identify all the proteins that are known to physically interact with viruses.

After reviewing tens of thousands of scientific abstracts, they culled the list to 1,256 proteins of interest.

“We identified 1,256 proteins that physically interact with viruses out of a total of 9,861 proteins with orthologs in the genomes of the 24 mammals included in the analysis,” the scientists said.

The next step was to build big-data algorithms to scour genomic databases and compare the evolution of virus-interacting proteins to that of other proteins.

The results revealed that adaptations have occurred three times as frequently in virus-interacting proteins compared with other proteins.

“We’re all interested in how it is that we and other organisms have evolved, and in the pressures that made us what we are,” said senior author Dr. Dmitri Petrov, also from Stanford University.

“The discovery that is in constant battle with viruses has shaped us in every aspect — not just the few proteins that fight infections, but everything — is profound.”



“All organisms have been living with viruses for billions of years; this work shows that those interactions have affected every part of the cell.”

Viruses hijack nearly every function of a host organism’s cells in order to replicate and spread, so it makes sense that they would drive the evolution of the cellular machinery to a greater extent than other evolutionary pressures such as predation or environmental conditions.

The study sheds light on some longstanding biological mysteries, such as why closely-related species have evolved different machinery to perform identical cellular functions, like DNA replication or the production of membranes.

Scientists previously did not know what evolutionary force could have caused such changes.
“This paper is the first with data that is large enough and clean enough to explain a lot of these puzzles in one fell swoop,” Dr. Petrov said.

Source: eLife

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