http://www.theatlantic.com/magazine/archive/2005/12/is-god-an-accident/304425/?single_page=true

But recently investigators have used the technique of showing them different events and recording how long they look at them, exploiting the fact that babies, like the rest of us, tend to look longer at something they find unusual or bizarre. This has led to a series of striking discoveries. Six-month-olds understand that physical objects obey gravity. If you put an object on a table and then remove the table, and the object just stays there (held by a hidden wire), babies are surprised; they expect the object to fall. They expect objects to be solid, and contrary to what is still being taught in some psychology classes, they understand that objects persist over time even if hidden. (Show a baby an object and then put it behind a screen. Wait a little while and then remove the screen. If the object is gone, the baby is surprised.) Five-month-olds can even do simple math, appreciating that if first one object and then another is placed behind a screen, when the screen drops there should be two objects, not one or three. Other experiments find the same numerical understanding in nonhuman primates, including macaques and tamarins, and in dogs. Similarly precocious capacities show up in infants' understanding of the social world. Newborns prefer to look at faces over anything else, and the sounds they most like to hear are human voices—preferably their mothers'. They quickly come to recognize different emotions, such as anger, fear, and happiness, and respond appropriately to them. Before they are a year old they can determine the target of an adult's gaze, and can learn by attending to the emotions of others; if a baby is crawling toward an area that might be dangerous and an adult makes a horrified or disgusted face, the baby usually knows enough to stay away.

...At this point the religion-as-accident theory says nothing about supernatural beliefs. Babies have two systems that work in a cold-bloodedly rational way to help them anticipate and understand—and, when they get older, to manipulate—physical and social entities. In other words, both these systems are biological adaptations that give human beings a badly needed head start in dealing with objects and people. But these systems go awry in two important ways that are the foundations of religion. First, we perceive the world of objects as essentially separate from the world of minds, making it possible for us to envision soulless bodies and bodiless souls. This helps explain why we believe in gods and an afterlife. Second, as we will see, our system of social understanding overshoots, inferring goals and desires where none exist. This makes us animists and creationists.

...But no scientist takes seriously Cartesian dualism, which posits that thinking need not involve the brain. There is just too much evidence against it.

Still, it feels right, even to those who have never had religious training, and even to young children. This became particularly clear to me one night when I was arguing with my six-year-old son, Max. I was telling him that he had to go to bed, and he said, "You can make me go to bed, but you can't make me go to sleep. It's my brain!" This piqued my interest, so I began to ask him questions about what the brain does and does not do. His answers showed an interesting split. He insisted that the brain was involved in perception—in seeing, hearing, tasting, and smelling—and he was adamant that it was responsible for thinking. But, he said, the brain was not essential for dreaming, for feeling sad, or for loving his brother. "That's what I do," Max said, "though my brain might help me out." Max is not unusual. Children in our culture are taught that the brain is involved in thinking, but they interpret this in a narrow sense, as referring to conscious problem solving, academic rumination. They do not see the brain as the source of conscious experience; they do not identify it with their selves. They appear to think of it as a cognitive prosthesis—there is Max the person, and then there is his brain, which he uses to solve problems just as he might use a computer. In this commonsense conception the brain is, as Steven Pinker puts it, "a pocket PC for the soul."

...The experimenters asked the children a set of questions about the mouse's biological functioning—such as "Now that the mouse is no longer alive, will he ever need to go to the bathroom? Do his ears still work? Does his brain still work?"—and about the mouse's mental functioning, such as "Now that the mouse is no longer alive, is he still hungry? Is he thinking about the alligator? Does he still want to go home?" As predicted, when asked about biological properties, the children appreciated the effects of death: no need for bathroom breaks; the ears don't work, and neither does the brain. The mouse's body is gone. But when asked about the psychological properties, more than half the children said that these would continue: the dead mouse can feel hunger, think thoughts, and have desires. The soul survives. And children believe this more than adults do, suggesting that although we have to learn which specific afterlife people in our culture believe in (heaven, reincarnation, a spirit world, and so on), the notion that life after death is possible is not learned at all. It is a by-product of how we naturally think about the world.

...Stewart Guthrie, an anthropologist at Fordham University, was the first modern scholar to notice the importance of this tendency as an explanation for religious thought. In his book Faces in the Clouds, Guthrie presents anecdotes and experiments showing that people attribute human characteristics to a striking range of real-world entities, including bicycles, bottles, clouds, fire, leaves, rain, volcanoes, and wind. We are hypersensitive to signs of agency—so much so that we see intention where only artifice or accident exists. As Guthrie puts it, the clothes have no emperor. Our quickness to over-read purpose into things extends to the perception of intentional design. People have a terrible eye for randomness. If you show them a string of heads and tails that was produced by a random-number generator, they tend to think it is rigged—it looks orderly to them, too orderly. After 9/11 people claimed to see Satan in the billowing smoke from the World Trade Center. Before that some people were stirred by the Nun Bun, a baked good that bore an eerie resemblance to Mother Teresa. In November of 2004 someone posted on eBay a ten-year-old grilled cheese sandwich that looked remarkably like the Virgin Mary; it sold for $28,000. (In response pranksters posted a grilled cheese sandwich bearing images of the Olsen twins, Mary-Kate and Ashley.) There are those who listen to the static from radios and other electronic devices and hear messages from dead people—a phenomenon presented with great seriousness in the Michael Keaton movie White Noise. Older readers who lived their formative years before CDs and MPEGs might remember listening intently for the significant and sometimes scatological messages that were said to come from records played backward.

...Sometimes there really are signs of nonrandom and functional design. We are not being unreasonable when we observe that the eye seems to be crafted for seeing, or that the leaf insect seems colored with the goal of looking very much like a leaf. The evolutionary biologist Richard Dawkins begins The Blind Watchmaker by conceding this point: "Biology is the study of complicated things that give the appearance of having been designed for a purpose." Dawkins goes on to suggest that anyone before Darwin who did not believe in God was simply not paying attention...Richard Dawkins may well be right when he describes the theory of natural selection as one of our species' finest accomplishments; it is an intellectually satisfying and empirically supported account of our own existence. But almost nobody believes it. One poll found that more than a third of college undergraduates believe that the Garden of Eden was where the first human beings appeared. And even among those who claim to endorse Darwinian evolution, many distort it in one way or another, often seeing it as a mysterious internal force driving species toward perfection. (Dawkins writes that it appears almost as if "the human brain is specifically designed to misunderstand Darwinism.") And if you are tempted to see this as a red state—blue state issue, think again: although it's true that more Bush voters than Kerry voters are creationists, just about half of Kerry voters believe that God created human beings in their present form, and most of the rest believe that although we evolved from less-advanced life forms, God guided the process. Most Kerry voters want evolution to be taught either alongside creationism or not at all...It's not surprising, then, that nascent creationist views are found in young children. Four-year-olds insist that everything has a purpose, including lions ("to go in the zoo") and clouds ("for raining"). When asked to explain why a bunch of rocks are pointy, adults prefer a physical explanation, while children choose a functional one, such as "so that animals could scratch on them when they get itchy." And when asked about the origin of animals and people, children tend to prefer explanations that involve an intentional creator, even if the adults raising them do not. Creationism—and belief in God—is bred in the bone.

From http://lesswrong.com/lw/7o4/atheism_the_autism_spectrum/6x1c :

Developmentally, children's reasoning about God's mental states, and about other non-physical agents, tracks the cognitive development of mentalizing tendencies [19], [20].

• Lane JD, Wellman H, Evans EM (2010) Children's understanding of ordinary and extraordinary minds. Child Dev 81: 1475–1489.

  How and when do children develop an understanding of extraordinary mental capacities? The current study tested 56 preschoolers on false-belief and knowledge-ignorance tasks about the mental states of contrasting agents—some agents were ordinary humans, some had exceptional perceptual capacities, and others possessed extraordinary mental capacities. Results indicated that, in contrast to younger and older peers, children within a specific age range reliably attributed fallible, human-like capacities to ordinary humans and to several special agents (including God) for both tasks. These data lend critical support to an anthropomorphism hypothesis—which holds that children’s understanding of extraordinary minds is derived from their everyday intuitive psychology—and reconcile disparities between the findings of other studies on children’s understanding of extraordinary minds.

• Taylor M, Carlson SM (1997) The relation between individual differences in fantasy and theory of mind. Child Develop 68: 436–455.

  The relation between early fantasy/pretense and children's knowledge about mental life was examined in a study of 152 3- and 4-year-old boys and girls. Children were interviewed about their fantasy lives (e.g., imaginary companions, impersonation of imagined characters) and were given tasks assessing their level of pretend play and verbal intelligence. In a second session 1 week later, children were given a series of theory of mind tasks, including measures of appearance-reality, false belief, representational change, and perspective taking. The theory of mind tasks were significantly intercorrelated with the effects of verbal intelligence and age statistically controlled. Individual differences in fantasy/pretense were assessed by (1) identifying children who created imaginary characters, and (2) extracting factor scores from a combination of interview and behavioral measures. Each of these fantasy assessments was significantly related to the theory of mind performance of the 4-year-old children, independent of verbal intelligence.

From http://james-g.com/2012/06/examining-idealism-part-3/ :

• Jaynes's The Mind Projection Fallacy (PDF)
• "to quote the philosopher Richard Joyce, from his book The Evolution of Morality:

Research reveals that “common-sense morality” does include certain claims to objectivity. One study (Nichols and Folds-Bennett 2003; Nichols 2004) looked at young children’s responses concerning properties such as icky, yummy, and boring and compared them with their attitudes toward moral and aesthetic properties. [...]

The children treated the instantiation of all properties as existentially independent of humans (i.e., before anyone was around, grapes were yummy, roses were beautiful, and so on), yet made a striking distinction between properties that depend on preferences and those that did not: Things that are yummy or icky are yummy and icky for some people, whereas things that are good are good “for real.” Having reviewed such evidence, Shaun Nichols (2004: 176) comes to this conclusion: “The data on young children thus suggest, as a working hypothesis, that moral objectivism is the default setting on common-sense metaethics.” […] Larry Nucci (1986, 2001) has even found that among Mennonite and Amish children and adolescents God’s authority does not determine moral wrongness. When asked whether it would be OK to work on a Sunday if God said so, 100 percent said “Yes”; when asked whether it would be OK to steal if God said so, over 80 percent said “No.” Such findings contribute to a compelling body of evidence that moral prescriptions and values are experienced as “objective” in the sense that they don’t seem to depend on us, or on any authoritative figure.