Are there no beneficial mutations?

[shunyadragon]

Source: https://www.sciencealert.com/researchers-have-found-a-brand-new-way-that-squid-can-edit-rna

Squids Can Edit Their RNA in an Unprecedented Way, Scientists Discover

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[rogue06]

Another example of a mutation that is beneficial, possibly even essential for our survival, later leading to problems.

Source: Humans Might Be So Sickly Because We Evolved to Avoid a Single Devastating Disease

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"Evolution gets the job done. But nobody said it was perfect." I can't remember who coined the description of biology being "gloriously messy" but that is exactly what it is -- especially when you are limited to modifying and adapting existent material.

In any case, the entire paper, "Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins" can be read HERE. This is the abstract from it:

Human-specific pseudogenization of the CMAHAlu-fusion-mediated loss-of-function of CMAHHomo

[shunyadragon]

Not if you can argue that degradative mutations predominate in selection.


No, Behe doesn't call any modification "degrading". He says that most variations that increase fitness are degradative.

Blessings,
Lee

Well, ah . . . your loaded question is trappy and misleading, The following may be helpful if you read the whole reference, which I dought you will.

Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871823/

The population genetics of mutations: good, bad and indifferent

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[shunyadragon]

But I need specific references!

Blessings,
Lee

Need reputable peer reviewed references, and not Behe with a religous agenda.

[rogue06]

I was switching through the channels this morning and as I came to one of the local religious channels I noticed that the host of the show was talking to a man wearing a lab coat. Since folks don't generally go around wearing lab coats it caught my interest so I stopped to see what was going on.




15. And the one that gets evolution deniers all worked up are the various mutations that confer resistance to malaria. Nearly everyone is aware of the sickle cell allele which confers resistance to malarial infections if you carry one copy of the allele but causes sickle cell anemia if you carry two copies. It's a good example of balancing selection. And even those with sickle cell anemia are considerably more likely to survive long enough to reproduce than those suffering from malaria.

What many are not aware of is that there are other alleles which confer resistance. The HbC variant for hemoglobin confers a 29% reduction in risk for malarial infection if you have one copy but a 93% risk reduction if you have two copies. The anemia resulting from the double copy of this gene variant is very mild in contrast to the debilitating effects of sickle cell.

Then there is the various types of Thalassemia. While they all have negative effects (bone deformities, and cardiovascular illness like anemia) it also confers a degree of protection against malaria (specifically, malaria caused by the protozoan parasite Plasmodium falciparum) and those with β-thalassemia apparently have some protection against coronary heart disease.

Finally, a single genetic mutation protects some African children from the deadly symptoms of malaria. The mutation occurs in the gene NOS2 that encodes an enzyme to produce the gas nitric oxide -- something that is present throughout the human body. The mutation is a polymorphism, a single letter change in DNA. It causes cells to ramp up production of the gas, which is thought to protect people against malaria.

Children in Tanzania and Kenya who have the mutation are much less likely to develop the disease than children who do not, with one study discovering that those with the mutation living in Tanzania were nearly 90% less likely to develop severe malaria than individuals without the mutation.

Researchers have discovered something similar among DNA variants that allowed our ancestors to survive the Black Death (which reduced the world's population from roughly 475 million down to 350 to 375 million and retuned periodically to kill millions more over the centuries) are linked to several diseases today.

Source: Autoimmune diseases tied to genes of Black Death survivors, study says

The Black Death, the 14th-century bubonic plague that killed some 1 in 3 people in Europe and an estimated 200 million across the world, has left another long-lasting mark: on the immune systems of people living today.

Four DNA variants appear to have helped boost survival rates from the plague — caused by a bacterium, “Yersinia pestis,” carried by small mammals and their fleas — in the mid-1300s and in recurring bouts of plague in later centuries, according to a recent study published in the journal Nature.

Researchers from the University of Chicago, McMaster University in Ontario and the Pasteur Institute in Paris say at least two of those variants associated with surviving the Black Death can be linked to autoimmune conditions common in modern society — including Crohn’s disease and rheumatoid arthritis.

Hendrik Poinar, a professor of anthropology at McMaster University and senior co-author on the study, said in the release that the research offered insight into “how pandemics can modify our genomes but go undetected in modern populations.”

Poinar noted that while the genes “provided tremendous protection during hundreds of years of plague epidemics,” they are linked to autoimmune disorders. “A hyperactive immune system may have been great in the past but in the environment today it might not be as helpful,” he said.

Having “two copies of a specific variant of one gene in particular, ERAP2, was strongly associated with surviving the plague,” according to a video published by the University of Chicago to explain the findings. People who survived the Black Death eventually passed the genetic variant to their children. Individuals who inherited such mutations were about 40 percent more likely to survive the plague, the research found.

Luis Barreiro, a professor of genetic medicine at the University of Chicago, said in a release on the study that the group’s findings served as “evidence that this one single disease event was enough to lead to selection in the human immune system.”

Barreiro said the findings were one of a kind. “This is, to my knowledge, the first demonstration that indeed, the Black Death was an important selective pressure to the evolution of the human immune system,” he said.

The medieval plague remains a topic of fascination among researchers and historians due to its “extensive demographic impact and long-lasting consequences,” the study notes, some 700 years after the deadliest pandemic recorded in history.

Researchers involved in the study analyzed high-quality genetic variation in more than 200 DNA samples extracted from the bones or teeth of individuals from Denmark and London who lived before the plague, died of it or lived between one and two generations after it swept the world.

There are different clinical forms of plague, though the most common are bubonic, pneumonic and septicemic, according to the Centers for Disease Control and Prevention. The Black Death, also referred to as the Pestilence, was a bubonic plague pandemic. Symptoms included skin tissue darkened by gangrene and swelling of lymph nodes, or buboes — the source of the term “bubonic.”

The plague strain eventually evolved into a less-dangerous variety, and today the protective variant is present in about 45 percent of British people, according to the 1000 Genomes database, Science Magazine reported in a write-up of the study. Deadly plague outbreaks remain a threat in some areas, but prevention and treatment methods have improved drastically, especially through the use of antibiotics.

The findings have raised the question: Will the coronavirus pandemic have a big impact on human evolution?

Fortune magazine reported that Barreiro is not convinced. The Black Death was far deadlier, he said, killing on scale orders of magnitude beyond the effects of covid-19, and had a more devastating effect on the young, killing people before they could pass on their genes.



Source

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The entire paper, Evolution of immune genes is associated with the Black Death can be read by clicking the link while the abstract is also available below

Abstract

Infectious diseases are among the strongest selective pressures driving human evolution^1,2. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis³. This pandemic devastated Afro-Eurasia, killing up to 30–50% of the population⁴. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.

[Roy]

Are you aware of the beneficial mutation observed during an experiment being run by the Discovery Institute?

[rogue06]

I probably should include this one as well, which I posted about in 2017

It appears that the people who live in the Quebrada Camarones region of Chiles Atacama desert have evolved a mutation that allows them to drink the water with high levels of arsenic (over 100 times the World Health Organizations safe limit) in it without ill effect.

Source: Human adaptation to arsenic in Andean populations of the Atacama Desert

Abstract

ObjectivesMaterials and Methods
The Chilean selected population samples come from Quebrada Camarones (n = 50) and the Azapa Valley (n = 47) in the north and San Juan de la Costa (n = 45) in southern Chile. The genotyping was conducted using PCR-RFLP. We compared the genotypic and allelic frequencies, and estimated the haplotype frequencies in the AS3MT gene.


Results
We found higher frequencies of the protective variants in those people from Camarones than in the other two populations. The haplotype estimation showed that the combination of protective variants of CTTA is very frequent in Camarones (68%) and Azapa (48%), but extremely low in San Juan de la Costa (8%). Also, the C variant associated with toxicity risks in the SNP Met287Thr had a lower frequency in Camarones (1%) and is higher in the other populations.

Discussion
The higher frequency of protective variants in both northern Chilean populations indicates a long exposure to naturally arsenic-contaminated water sources. Our data suggest that a high arsenic metabolization capacity has been selected as an adaptive mechanism in these populations in order to survive in an arsenic-laden environment.



Source

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As an article in New Scientist explains:

The body uses an enzyme called AS3MT to incorporate arsenic in two compounds, monomethylarsonic (MMA) acid and dimethylarsinic (DMA) acid. People who metabolise arsenic more efficiently convert more of it into the less toxic, more easily expelled DMA.

Mario Apata of the University of Chile in Santiago and his colleagues looked at variations in the gene coding for AS3MT in nearly 150 people from three regions of the country. They found higher frequencies of the protective variants in people from Camarones: 68 per cent there had them, as opposed to just 48 and 8 per cent of people in the other two. Our data suggest that a high arsenic metabolization capacity has been selected as an adaptive mechanism in these populations in order to survive in an arsenic-laden environment, the researchers conclude (American Journal of Physical Anthropology, doi.org/bz4s).

The variants that protect the Camarones people are called single nucleotide polymorphisms changes in a single DNA letter of the genetic code. Anthropologist Lorena Madrigal of the University of South Florida in Tampa says these are such tiny mutations that they arent telling us exactly how the changes affect the enzyme molecule and its detoxifying effects.

Previous studies found similar mutations in the AS3MT gene that contribute to improved arsenic metabolisation in Vietnam and Argentina. Sequencing the entire chromosomal region around this gene could reveal more, but theres still a long way to go before we fully understand the molecular mechanism for how arsenic resistance works.

Though its a fascinating example of what appears to be contemporary evolution in humans, it also underscores the water quality problems that many populations face, says Madrigal. And many may not be able to evolve to deal with it.

[Roy]

I probably should include this one as well, which I posted about in 2017

I wonder if those variants exist in Bangladesh.

[rogue06]

I wonder if those variants exist in Bangladesh.

I've heard that portions of the country have water with a high arsenic content, are those drinking it suffering no deleterious effects?

[Roy]

I've heard that portions of the country have water with a high arsenic content, are those drinking it suffering no deleterious effects?

No, they're suffering lots of deleterious effects. Those variants would, if they exist there, be highly favoured.

(The problem is not that the water there has a high arsenic content, it's that dense populations are using so much water that wells are having to be deepened into arsenic bearing strata.)

[rogue06]

No, they're suffering lots of deleterious effects. Those variants would, if they exist there, be highly favoured.

(The problem is not that the water there has a high arsenic content, it's that dense populations are using so much water that wells are having to be deepened into arsenic bearing strata.)

It goes to show that just because an organism (in this case, us) has a need for some sort of mutation doesn't mean it will take place.

[rogue06]

An article discussing several beneficial mutations in humans, including a few not previously mentioned

Source: 8 Genetic Mutations That Can Give You 'Superpowers'

More than 99 percent of your genetic information is exactly the same as every other person on the planet. Your genes determine your skin colour, sex, and hair colour and whether or not you have certain genetic diseases.

But it's in that less than 1 percent that things get interesting. Specific genetic variations allow some of us to acquire certain - dare we say super - qualities. Here are the ways our genes can predispose us to have special abilities.

ACTN3 and the super-sprinter variant

We all have a gene called ACTN3, but certain variants of it help our bodies make a special protein called alpha-actinin-3. This protein controls fast-twitch muscle fibres, the cells responsible for the speedy tensing and flexing of the muscles involved in sprinting or weight-lifting.

This discovery, which happened around 2008 when geneticists studying elite sprinters and power athletes found that very few among them had two defective ACTN3 copies, is what led to the gene being dubbed the 'sports gene'.

Among the general population, however, some 18 percent of us are completely deficient in the speedy-muscle-contracting protein - we inherited two defective copies of ACTN3.

hDEC2 and the super-sleeper mutation

Imagine if you could feel totally energised on just 4 hours of sleep each night. Some people are naturally that way.

These people are called 'short-sleepers', and scientists are only recently uncovering what exactly predisposes them to be this way.

For the most part, researchers believe that the capabilities are connected to specific genetic mutations, and have publicly identified one on the hDEC2 gene.

That means that short-sleeping habits can run in the family, and scientists hope to one day learn how to harness this ability so it can be used to help people switch up their sleeping routines.

TAS2R38 and the supertaster variant

About a quarter of the population tastes food way more intensely than the rest of us.

These 'super tasters' are more likely to put milk and sugar in bitter coffee, or avoid fatty foods. The reason for their reaction, scientists think, is programmed into their genes, specifically one called TAS2R38, the bitter-taste receptor gene.

The variant responsible for super tasting is known as PAV, while the variant responsible for below-average tasting abilities is known as AVI.

LRP5 and the unbreakable mutation

Brittle bones pose a big problem. Researchers have identified a genetic mutation on the LRP5 gene that regulates bone-mineral density, which can cause brittle, weak bones.

So far, scientists have identified multiple mutations to the LRP5 gene that appear to be linked with bone conditions, including juvenile primary osteoporosis and osteoporosis-pseudoglioma syndrome.

But a different type of mutation on the same gene could also have the opposite effect, giving some people extremely dense bones that are practically unbreakable.

The malaria-protecting variant

People who are carriers for sickle-cell disease - meaning that they have one sickle gene and one normal haemoglobin gene - are more protected against malaria than those who are not.

Though blood disorders are not necessarily 'super', this information may influence more innovative malaria treatments down the road.

CETP and the low-cholesterol mutation

Although environment - including what we eat - can influence cholesterol levels, genetics play a big role, too.

Mutations in a gene responsible for producing a protein called cholesteryl ester transfer protein (CETP) result in a deficiency of that protein. CETP deficiency is linked with having higher levels of 'good' HDL cholesterol, which helps carry cholesterol to the liver so it can be removed from the body, resulting in lower cholesterol levels.

Studies have also found a lower prevalence of coronary heart disease in people with the deficiency-causing mutation.

BDNF and SLC6A4 and the super coffee-drinker variants

There are at least six genes associated with how your body processes caffeine.

Some variants, near the genes BDNF and SLC6A4, influence the rewarding effects of caffeine that make you want to drink more.

Others are linked to how the body metabolises caffeine - those who break caffeine down more quickly may be more likely to drink more of it because the effects wear off faster.

Others still help explain why some people are able to fall asleep at night after their daily morning coffee while others have to cut out the habit altogether to get a good night's sleep.

ALDH2*2: The super-flusher variant

Do your cheeks go rosy shortly after having a single glass of wine? A mutation on the ALDH2 gene may be the culprit.

One such mutation interferes with the ability of a liver enzyme called ALDH2 to convert the alcohol byproduct acetaldehyde into acetate.

When acetaldehyde builds up in the blood, it opens up the capillaries, causing what we see as a flush or glow.

But there's another dangerous component of acetaldehyde - it's a carcinogen in people, and research suggests that people who flush when they drink alcohol may have the mutation and may also be at a greater risk of esophageal cancer.



Source

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