Monthly Archives: August 2014

This blog article is worth reblogging. The authors demonstrate, among many things, that the so-called DNA junk is not junk seen from DNA’s own perspective. Repetition (i.e. copying) of the same sequencies increases the chances for the gene(s) involved of not being wiped out or eliminated. Cf. the term “The selfish gene”.

Life doesn’t make trash

A genome is not a blueprint for building a human being, so is there any way to judge whether DNA is junk or not?

Illustration by Matt W. Moore

Illustration by Matt W. Moore

Itai Yanai is associate professor in biology at the Israel Institute of Technology.

Martin Lercher is professor at the Institute of Bioinformatics in Dusseldorf, Germany. Lercher and Yanai are co-authors of the forthcoming book, The Society of Genes, from Harvard University Press.

Could all this mysterious ‘dark matter’ in our genome really be non-functional?

To answer this question, hundreds of scientists worldwide joined a massive science project called the Encyclopedia of DNA Elements, or ENCODE. After working hard for almost a decade, in 2012 ENCODE came to a surprising conclusion: rather than being composed mostly of useless junk, 80 per cent of the human genome is in fact functional.

To reach that conclusion, ENCODE systematically scouted the genome as a whole for specific functions. One function could be coding for proteins; another function could be acting as a ‘molecular switch’ that regulates the operation of other genes. In one experiment, for example, ENCODE surveyed the entire genome for DNA that is bound by ‘transcription factors’ – proteins known for calling other genes into action. In this way, ENCODE compiled a comprehensive and very useful catalogue that provided a functional clue for 80 per cent of the 3 billion nucleotides that comprise all the genes of the human genome. The ENCODE results seemed to confirm that our genome is indeed a tidy blueprint; that almost every bit of the human genome is there for a reason, and that our genetic heritage is not a small heap of information buried under a pile of junk.

Consider the so-called ‘LINE-1 elements’, a DNA sequence formerly classed as junk. Our genome teems with 500,000 copies of this 6,000-letter sequence that seems to do nothing but reproduce copies of itself, the very definition of the ‘selfish gene’. According to ENCODE, these LINE-1 elements are functional since they are biochemically active. But does this mean they function to further human survival itself?

Likely not. ‘Function’ is a loaded word, and ENCODE chose a very inclusive definition: in the ENCODE world, function can be ascribed to any stretch of the genome that is related to a specific biochemical activity. But such inclusiveness can lead to ridiculous conclusions. To make an analogy, consider spam emails. What spam emails mostly do is occupy email servers that aim to separate them from genuine email. Few people would argue that occupying spam filters is a function of spam – but an ENCODE-like definition would say just that. Indeed, many of ENCODE’s 80 per cent ‘functional elements’ are unlikely to contribute to human survival and the reproduction of human genomes, which is what you would expect if you consider function from the perspective of a human blueprint.

Yet viewing our genome as an elegant and tidy blueprint for building humans misses a crucial fact: our genome does not exist to serve us humans at all. Instead, we exist to serve our genome, a collection of genes that have been surviving from time immemorial, skipping down the generations. These genes have evolved to build human ‘survival machines’, programmed as tools to make additional copies of the genes (by producing more humans who carry them in their genomes). From the cold-hearted view of biological reality, we exist only to ensure the survival of these travellers in our genomes.

This is the central idea in Richard Dawkins’s milestone book,The Selfish Gene (1976), and the fundamental shift in perspective it entails might be as hard to accept as it was hard to acknowledge that our world revolves around the sun, not the sun around us. The selfish gene metaphor remains the single most relevant metaphor about our genome.

Building on the work of generations of biologists since Charles Darwin, Dawkins took the theory of evolution to its logical conclusion. Darwin’s greatest contribution to science was the concept of natural selection: the fundamental logical principle that inevitably causes a population to gradually adapt to its environment. At first, variation arises in individuals as genes mutate randomly over time. Then, through the mindless process of natural selection, some individuals fare better than others in the task of surviving and reproducing because of differences in their genes, which are then passed on.

What we see are not the real players of the game of life; we just see the consequences as those players strategize to stay in the game.

Darwin showed that one simple logical principle could lead to all of the spectacular living design around us, including humankind, previously believed to have been specially created in the image of a god. The logic of natural selection applies far beyond the evolution of species: anything that is good at replicating itself promotes its own survival.

Our genomes are reassembled from the genes found in our parents’ genomes at each generation: when your mother and father prepared the DNA passed on to you, they recombined the genome copies they inherited from their own parents into new combinations. From the viewpoint of natural selection, each gene is a long-lived replicator, its essential property being its ability to spawn copies. In order to spawn copies, many genes have evolved functions important for the survival of the organism in which they reside. Those genes that fail at replicating are no longer around, while even those that are good face stiff competition from other replicators. Only the best can secure the resources needed to reproduce themselves.

It is those replicators that are at the heart of the natural world, that jump from generation to generation, abusing us (or any other species) as their survival machines. When looking at our genome, we might take pride in how individual genes co-operate in order to build the human body in seemingly unselfish ways. But co-operation in making and maintaining a human body is just a highly successful strategy to make gene copies, perfectly consistent with selfishness.

So why are we fooled into believing that humans (and animals and plants) rather than genes are what counts in biology? It is a matter of scale: the world we can see is too big to include genomes, and our lifespan is too short to see how individual genes come into existence, change, and disappear again, processes that unfold over millions of years. What we see are not the real players of the game of life; we just see the consequences of their strategies to stay in the game.

Many genes in our genomes survived because they contributed to making better survival machines – humans better at spreading those genes. But what about the alleged junk, what about, for example, the 500,000 LINE-1 elements? The answer is beautifully simple: each LINE-1 element consists of a set of genes. Together, these encode proteins that execute a molecular programme of inserting additional copies of itself into the genome – a grandiose ‘copy-paste’ strategy. The fact that there are 500,000 copies of them is a testament to their successful proliferation programme. By copying themselves into the genome over and over again, LINE-1s ensure that they remain associated with those genes that make the survival machine.

Even if a large number of LINE-1 copies are removed, lost, or damaged by mutations, there will always be more copies somewhere else in the genome. This is the only explanation needed to justify the LINE-1s’ continued existence. They don’t need to have a specific function in the human blueprint at all – they are freeloaders. ENCODE, however, would reason that these DNA segments are functional since they engage in the process of transcription, whereby a molecular template of the gene works to churn out more of the same. Thus, while most LINE-1s are no longer even capable of making proteins, ENCODE would conclude that they are part of the human blueprint.

To emphasise this point, consider another kind of junk in the genome, the ‘Alu’ element, about 300 letters long. Each of your two genome halves contains 1 million copies of this gene. What does it do? Looking at Alu’s sequence reveals a very uninteresting gene. The only exception is the very last part of its sequence: it matches precisely the last section of LINE-1 elements. In LINE-1s, this stretch of letters is used as a signal, so that the LINE-1 proteins know which sequence they should copy back into another genomic location. By having the same signal, Alus effectively masquerade as LINE-1 elements, fooling the LINE-1 machinery into copy‑pasting them into the genome. It turns out that the freeloaders themselves have freeloaders!

At the most fundamental level, then, our genome is not a blueprint for making humans at all. Instead, it is a set of genes that seek to replicate themselves, making and using humans as their agents. Our genome does of course contain a human blueprint – but building us is just one of the things our genome does, just one of the strategies used by the genes to stay alive. In their selfish desire to leave offspring, our genes have evolved to form a society where they work together efficiently, dividing the labour to ensure that each makes it into the next generation. Like Adam Smith’s invisible hand, the genes in this society co-operate with one another not from a sense of fairness or design, but simply to maximise their own survival. From the myriad interactions of genes in this complex society emerge the striking biological adaptations we see in the living world.

Junk is not trash, and it might come in handy at some point, even if that is not its function

Our genome is filled with freeloaders that manage to hang on, simply because the damage they do is not large enough to make the effort to weed them out worthwhile for other genes, or because their strategy for survival is so conniving that they are difficult to expel. From the point of view of the society of genes, any freeloader DNA – DNA that does not contribute to the genome’s ability to leave offspring, that is, any DNA that does not contribute to organising our bodies – is junk.

ENCODE has called 80 per cent of the human genome functional, yet 97 per cent of the genome does not encode proteins or other molecules that support human life. Is all this DNA just junk? Of course not. There are undoubtedly many molecules whose function we have not yet grasped. And a blueprint alone is not enough to build anything – you also need assembly instructions and a time plan that orchestrates the building process. The portion of the genome responsible for this organisational feat likely adds another 7 per cent or so to the blueprint’s 3 per cent, leading scientists to suspect that about 10 per cent of the genome is actually needed to specify a functioning human.

There is good evidence for this 10 per cent. If we compare our genome to that of other mammals, we find that 90 per cent of the genome was free to change through random mutations. Those DNA letters apparently did not contribute to the efficiency of the survival machine, us. By contrast, mutations in the remaining 10 per cent were weeded out by natural selection because they would have compromised the DNA sequences’ ability to spread – either by damaging the survival machine’s functioning, or by reducing the sequences’ freeloading capacity. This is the definition of function that has traditionally been used by evolutionary biologists as well as by philosophers of science: if something is conserved by natural selection, then it is functional. Function, then, is identified as the feature that ensures the spread or maintenance of a particular DNA sequence.

Junk is not trash and, as the Nobel laureate and genetics pioneer Sydney Brenner has pointed out, it might come in handy at some point, even if that is not its function. Any stretch of DNA can by accident turn into something that then contributes to the spread and survival of the genome. And sure enough, we do, for example, find individual LINE-1 or Alu sequences whose insertion has changed the expression of neighbouring genes in useful ways. These few members of the freeloader community effectively switched sides: they became part of the society of genes that provides the blueprint for human life.

But such examples don’t mean that our genome hordes junk because it might become useful in some future situation – the vast majority of repeats freeload off our bodies, the survival machines built by a co-operative society of genes. To explain why these junkish repeats litter our genome, we do not need to search for any other explanation, any other function, than their capacity to ensure their own persistence in the society of genes.

A misunderstanding persists in the wrong-headed notion that our genome encodes the blueprint of human life. It does not. The blueprint analogy does not apply to the majority of our genome, nor is the non-blueprint component useless junk. Someone or something benefits from much of this genetic code, but value is in the eye of the beholder. For the majority of functional repeats such as Alu and LINE-1, the only beneficiaries are they themselves; attributing human benefit to junk imagines harmony and purpose where none exist. The truth is that many DNA sequences have survived inside our genome going all the way back to the first replicators, through aeons of evolutionary time.

What a piece of work!

25 August 2014

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Easter: Was the Risen Jesus Originally Female?

Many ancient religions, including early Hebrew and European pagan traditions, evolved in part out of star worship. That is, the stars up in the sky were seen as gods and goddesses (cf. the zodiac and astrology).

Did you know that our Easter holiday is named after an Anglo-Saxon fertility goddess alternately known as Estre, Eostre, and Ostara.

The story of the Sumerian goddess Inanna (in the East Semitic Akkadian, Assyrian and Babylonian regions that same goddess was called Ištar or Ishtar) can be seen as sort of a prototype or model for the formation of Bible-Jesus.

Read more about all the similarities in this article. (You’ll find more information on Wikipedia, see: http://en.wikipedia.org/wiki/Inanna and http://en.wikipedia.org/wiki/Ishtar .

ValerieTarico.com

Ishtar--the goddess who became the resurrected Jesus? Ishtar–the goddess who became the resurrected Jesus?

An interview with Dr. Tony Nugent, ordained minister, scholar of world religions, and symbologist. 

Many ancient religions, including early Hebrew and European pagan traditions, evolved in part out of star worship.  Because so many traditions treated celestial events including the solstices and equinoxes as auspicious, it can be hard to tease out which holiday traditions originated where.  But even Church authorities say that our Easter holiday was named after an Anglo-Saxon fertility goddess alternately known as Estre, Eostre, and Ostara.

Over time, religious traditions tend to merge and blend, which the Catholic church saw as an opportunity rather than a problem. Authorities advised early missionaries simply to retain local holidays and rituals and give them new meaning.  A letter from Pope Gregory I to St. Mellitus, credited with Christianizing England, suggested that it would be easiest to convert the heathen Anglo-Saxons this way.

In pre-Christian Europe, Lent, which originally meant no more than…

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Ancient Mythic Origins of the Christmas Story [and Angels]

The familiar Christmas story, including the virgin conception and birth of Jesus, is found only in the gospels of Matthew and Luke.

You should ask yourself: How come this miraculous event isn’t mentioned at all in the rest of the New Testament?

Therefore it can’t be dismissed that the details of the Nativity story are kind of interpolations, i.e. information added later on to underline and emphasize Jesus’ divine origin. (Maybe that’s why Matthew and Luke have inconsistent details in their Native stories. for example contradictory genealogies. Different story lines usually give us different details backing up the same story.

In this same article you can also read about the origin of angels. How our views of the angels have shifted throughout the angelic history (from being gods to becoming aides and messengers to the one God in Heaven).

 

ValerieTarico.com

Christmas - nativity sceneValerie Tarico interviews Dr. Tony Nugent, scholar of world religions. Dr. Nugent is a symbologist, an expert in ancient symbols. He taught at Seattle University for fifteen years in the Department of Theology and Religious Studies and is an ordained Presbyterian minister.

Many Americans have heard that December 25 was a birthday of Roman gods long before it was chosen to celebrate the birth of Jesus. Some people also know that our delightful mélange of Christmas festivities originated in ancient Norse, Roman and Druid traditions – or, in the case of Rudolph, on Madison Avenue. But where does the Christmas story itself come from: Jesus in the manger, the angels and wise men?

Nugent: The familiar Christmas story, including the virgin conception and birth of Jesus, is found in the gospels of Matthew and Luke. Scholars have pointed out that these stories are somewhat disconnected from other parts of…

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Surprise! It’s Possible Jesus Never Existed

The notion that Jesus never existed is still a minority position.nevertheless many Bible stories like the virgin birth, miracles, resurrection, remind us of mythic themes known from tales of other deities. As a matter of fact such borrowing and rework of mythic themes were not at all uncommon in the Ancient Near East region.

So calling the gospel stories historicized mythology is actually a hypothesis that can’t be excluded or repudiated.

In this intriguing article five arguments are listed and discussed by the author Valerie Tarico.

The five arguments can be summarized like this:

1. No first century secular evidence whatsoever exists to support the actuality of Yeshua ben Yosef a.k.a. Jesus (Christ).

2. The earliest New Testament writers seem ignorant of the details of Jesus’ life, which become more crystalized in later texts.

3. Even the New Testament stories don’t claim to be first-hand accounts.

4. The gospels, our only accounts of a historical Jesus, contradict each other.

5. Modern scholars who claim to have uncovered the real historical Jesus depict wildly different persons.

ValerieTarico.com

Mythical JesusMost antiquities scholars think that the New Testament gospels are “mythologized history.”  In other words, they think that around the start of the first century a controversial Jewish rabbi named Yeshua ben Yosef gathered a following and his life and teachings provided the seed that grew into Christianity. At the same time, these scholars acknowledge that many Bible stories like the virgin birth, miracles, resurrection, and women at the tomb borrow and rework mythic themes that were common in the Ancient Near East, much the way that screenwriters base new movies on old familiar tropes or plot elements. In this view, a “historical Jesus” became mythologized.

For over 200 years, a wide ranging array of theologians and historians—most of them Christian—analyzed ancient texts, both those that made it into the Bible and those that didn’t, in attempts to excavate the man behind the myth.  Several current or recent bestsellers…

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King’s College London comes to its senses, deep-sixes postgraduate theology curriculum

Two quotes from this blog article that conveys, IMO, very pleasant news for all non-God believers.

1) What a good feeling it is to see a university get rid of its theology courses! Religious history or comparative religion is fine; theology, not so much. If you want to teach about the properties of nonexistent objects, do it in a private divinity school or seminary.

2) It’s an embarrassment to Oxford and other state-supported schools in the UK that they would even have programs in theology, and this has always baffled me. It may be a holdover from the days when those schools were actually religious institutions, but in a modern world there’s no excuse for it. In fact, having theology programs in public universities would be illegal in the U.S., as it would constitute an illegal violation of the First Amendment (public endorsement of religious doctrine).

NOW I wonder: When will the same thing happen here in Sweden?

Why Evolution Is True

What a good feeling it is to see a university get rid of its theology courses! Religious history or comparative religion is fine; theology, not so much. If you want to teach about the properties of nonexistent objects, do it in a private divinity school or seminary. There’s simply no excuse for a public university to act as if superstition is real; it’s as if they had an entire curriculum devoted to ghosts, their properties, and their wishes, and pretended they were studying real objects! Or an entire curriculum on homeopathy in or alongside a medical school.

But King’s College London has made the decision, although it was ostensibly made on financial grounds. According to The Tablet(a Catholic news weekly),

Leading theologians have criticised the closure of a university’s post-graduate theology and ministry programme as “deeply regrettable”.

(Note that there are also “ministry” courses, so King’s College is also in…

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Woo-wooprofilering

Gesus shows in this blog, published on his own blog GesusBloggen, some characteristics or personality traits that are typical of woos . Very interesting, indeed! There are also many comments to that blog. One of the many commenters is bbnewsab, i.e. me. I present some links to articles about why it’s so easy to believe in magical and religious thinking.
BTW, you can read more about magical and religious thinking by clicking this link: http://en.wikipedia.org/wiki/Magical_thinking .

Gesusbloggen

Tänkte man kunde göra en gärningsmannaprofil på en typisk woo-woo, en såkallad Woo-wooprofil.

Woo-wooprofilering bygger på beteendevetenskap där man studerar de mest troliga demografiska, sociala och beteendemässiga egenskaper som gärningskvinnan bakom ett woo kan tänkas ha ;-]

Man förutsätter att hur en person agerar överensstämmer med personens personlighet. Utifrån känd information om var, när och hur ett woo utförts försöker kriminalpoliser, rättspsykiatriker och rättspsykologer tillsammans beskriva troliga personliga egenskaper hos gärningskvinnan. Denna profil sammanställs sedan med vetenskapliga erfarenheter av vilka människor som beter sig likartat.

En riktig woo-woo, mest troligt:
woo-wooprofil
– Är kvinna
– Är runt 40 – 50
– Är frånskild ev omgift
– Har varit hemma med barn
– Har äldre, ev “utflugna”, barn
– Kan “gått in i väggen” tidigare
– Är eller har varit sjukskriven
– Är “vilsen” och ev ensam
– Har en eller flera katter
– Söker efter någon mening med livet
– Har…

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Just weeks after converting to Islam, Daniel Munoz blamed killing his wife on the voice of Allah, Australian court told

Not at all surprising. Voice hearing is often a sign of psychosis. And religious fanaticism is sort of a mental disease disease in itself. Cf. this article by Patrick McNamara: The god effect (see: http://aeon.co/magazine/psychology/dopamine-marks-the-line-between-religious-believer-and-fanatic/ ).

Religion spawns both benevolent saints and murderous fanatics. Patrick McNamara ia asking: Could it be different dopamine levels in the brain that drive that switch? Especially in a neural circuit/network involving strong connection between the amygdala, the nucleus accumbens and parts of the prefrontal cortex (PFC).

The amygdala is responsible for emotional activity and reactivity. Specific areas of the PFC are associated with emotion regulation and critical thinking skills.The nucleua accumbens is center for reward sensitivity. Too much activity (= hyperactivity) in this brain circuitry/network makes you over-creative (= you’re not inhibited by any limitations), which in turn can transform you to a (religious) fanatic.

The Muslim Issue

Daniel Munoz allegedly claimed Allah told him to kill his wife.Daniel Munoz allegedly claimed Allah told him to kill his wife.

DAILY TELEGRAPH, AUSTRALIA

A SYDNEY man stabbed his wife to death just weeks after converting to Islam — claiming he did it in the name of Allah, police allege.

“Allah told me to kill her,’’ Daniel Munoz allegedly said when questioned by police over the stabbing death of Melissa Munoz on October 20 last year.

Mrs Munoz had taken out a number of apprehended violence orders against her husband of 22 years after feeling threatened by him.

Police said the unemployed Munoz went to the family home in Hobartville in Sydney’s northwest where, at about 3.30pm, screams were heard.

Munoz is accused of standing over the 40-year-old mother of seven in the loungeroom of the home, holding her by her hair and stabbing her more than 10 times to the head and chest with a knife he had taken…

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Sir Arthur Conan Doyle and the Spirits

Sir Arthur Conan Doyle is also known for his belief in spirits and fairies. His credulity seemed almost infinite. By the time he published The History of Spiritualism, most of the mediums he discusses in that book had been exposed resorting to fraud, in some cases repeatedly. Some of the mediums had even confessed. None of this deters him. He is able to defend the supernatural abilities of anyone who seems to display gifts that in some way bolster his religious beliefs in a spirit world.

Skeptical Humanities

Note: The following essay is based on a segment from Skepticality.

Sir Arthur Conan Doyle is known for many things: the creation of Sherlock Holmes, a spectacular mustache, and his belief in spirits and fairies.

Sir Arthur Conan Doyle and Hairy Friend Sir Arthur Conan Doyle and Hairy Friend

M’colleague, Bob Blaskiewicz, has discussed Doyle’s* seemingly ludicrous belief in the Cottingley fairies, but spiritualism was Doyle’s burning passion. He possessed a religious, missionary, perhaps even messianic zeal to promote belief in discarnate spirits and life after death. He lectured and wrote voluminously on the subject, including a two volume History of Spiritualism.

It’s easy to make fun of Doyle’s beliefs. Really easy. Stunningly easy. In fact it’s quite hard to refrain from making fun of them. In his writings on spiritualism, he displayed the same degree of levelheadedness and perspicacity that led him to conclude that this is an actual picture of a fairy:

"And his mustache is THIS big!" “And…

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Lite själ igen

Christer Brodén om begreppen själ och ande. Ett citat ur artikeln: Asaguden Heimdal, det har jag nämnt förut, tros kunna ha en förhistoria som solgud under bronsåldern. Rig är ett annat namn på honom, som på sanskrit, ett annat och riktigt forntida indoeuropeiskt språk, betyder medvetande, d.v.s. den seende och tänkande.

Blickens Äventyr

Glömska

Arkeologen Marija Gimbutas hör till dem som tror, att skrivkonsten och andra färdigheter uppfunnits och glömts bort och på nytt uppfunnits under vår historia. Det är hypoteser, men för mig känns de trovärdiga.

Begreppen själ och ande har fyllt med otaliga tankar de senaste årtusendena. Även sådana tankar glöms bort och nya skapas. Orden kan däremot leva kvar. Mitt ofta framförda paradexempel är ett av Guds namn i Bibeln, Shaddaj. Det var tidigare namn på en mångud i staden Ur, som Abraham kom från.

Vad själ och ande haft för betydelse under årtusendena kan nog vara väldigt svårt att reda ut. Jag fick min idé om en tidig betydelse hos de där två begreppen, en gång när jag såg bilden av ormgudinnan från Kreta. Den bilden har jag haft med många gånger.

knossos21c-2

Stenarna på Gotland

Den överensstämmer ju med bildstenen från Smiss, som jag också visat här flera…

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Wellcome Trust Research Round-Up: 18/08/14

Neuroscientific news from Wellcome Trust Research:

1) Mind and body: link between immune system and mental health

2)Momentary subjective well-being: a mathematical equation to predict happiness

3)Toxic proteins implicated in brain diseases

Wellcome Trust Blog

Our fortnightly round-up up of news from the Wellcome Trust research community…

Mind and body: link between immune system and mental health

The immune system may have a role to play in mental illness, suggests research from the University of Cambridge, published in JAMA Psychiatry last week.

With funding from the Trust, as well as the NIHR and the MRC, the team from Cambridge carried out the first ever longitudinal study to examine the link between inflammatory markers, such as the protein interleukin-6 (IL-6), in childhood and subsequent mental illness.

ALSPAC - Children of the 90sThey took blood samples from 4,500 individuals (from the Avon Longitudinal Study of Parents and Children, or Children of the 90s), at age 9 and followed up at age 18 to see if they had experienced episodes of depression or psychosis. They found that those participants whose levels of IL-6 were deemed ‘high’ when children were nearly twice as likely to…

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