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Our future, our universe, and other weighty topics

Wednesday, January 30, 2019

The Science-Flavored Guesswork Known as Phylogenetics

Our scientists often give us visual displays designed to impress us with their grasp of nature. Such visuals should often be taken with a large grain of salt. An example is the type of “composition of the universe” pie graph that claims the universe is about 72% dark energy, 23% dark matter and 5% regular matter. As discussed here, the case for dark matter is wobbly. Moreover a 2016 study has cast doubt on the research used to make the claim that the universe is 72% dark energy, raising doubts about whether dark energy even exists.

Another type of scientific visual we should have little trust in are those visuals showing a kind of “tree of life” that supposedly shows how one type of life evolved into another. Such visuals are generated using what is called phylogenetics, which involves attempts to compute the ancestry of living things from studying their genomes.

There is a gigantic amount of data involved in the genome of a single organism. Comparing the genomes of many different organisms for similarities becomes a task too data-intensive for a person to do in his own head or on paper. When you get into the task of estimating hypothetical inheritance trees, the number of possibilities becomes so gigantic that the task becomes something so difficult that it is often handled by computers.

The idea of doing computer analysis on genomes may sound very impressive, but there are several reasons why this type of analysis does not in general provide convincing evidence that some species  had a particular ancestry.

1. Phylogenetic programs assume common descent rather than prove it.

The computer programs used for phylogenetic analysis are not programmed to analyze the likelihood that a particular set of species share a common ancestor. Instead, such programs typically assume from the beginning that such species do share a common ancestor, and the programs busy themselves with trying to compute the most probable inheritance tree that can link such species. 

2. Phylogenetic programs compute a “most likely” tree of evolution, but such a tree is not a likely “tree of evolution.”

One must be careful to distinguish between the concept of “most likely” and “likely.” “Likely” means having a probability of greater than 50%. But “most likely” means more likely than any other possibility. It is very common for a “most likely” possibility to be unlikely, with a probability of less than 50%. For example, if you choose a random word from a book, the “most likely” choice is the word “the.” But such a choice is not a likely choice, and has a likelihood of less than 10%.

In the case of a phylogenetic software, it will not produce an inheritance tree that is likely to be correct. It will merely produce an inheritance tree that may be the “most likely” among many different alternatives that the software explores. But such a tree may still be very unlikely to be accurate.

3.With any complicated inheritance tree problem, there is a “combinatorial explosion” that prevents phylogenetic programs from being able to try all possibilities, so the software resorts to a fragmentary exploration of the solution space.

Anyone who has studied computer science knows that when there are many variables or data points, the number of possible arrangements increases exponentially. A classic example is what is known as the traveling salesman problem. If a salesman has to travel to 20 cities, then the total number of possible travel routes is roughly 20 factorial, which is too large a number to compute.

Given more than 200 species, the possible number of inheritance trees to be considered becomes so great there is no possible way for any computer program to compute all the possibilities. So phylogenetic programs typically resort to a shortcut. They simply allow you to try a certain number of possibilities, and rate each one for its likelihood. The one with the best rating is singled out as the winner. But that's not a method that should inspire confidence. The winner is unlikely to be the actual inheritance tree for the set of species, whenever there are many species being considered.

4. Too few living species have had their genomes analyzed for phylogenetic programs to be very reliable.

According to this government web site, “more than 250” animal species have had their genomes analyzed. The problem for phylogenetic programs is that this is but a tiny fragment of the total number of living species, which has been estimated as 8 million. Consequently, we don't have the data to be reliably calculating an inheritance tree based on so few genomes. Perhaps after very many thousands of genomes have been cataloged, such analysis may be more reliable.

5. We don't have any DNA data for even 1% of the species that previously existed.

The reliability of phylogenetic programs is proportional to how much DNA data we have for extinct species that lived long ago. But we have very, very little DNA data for species that lived long ago. The half-life of DNA is only 521 years, meaning every 521 years half of the DNA information will disappear. So we have no DNA information for species such as dinosaurs. There is no truth to the idea that dinosaur DNA has been preserved because insects that bit dinosaurs have been preserved in amber.  That's a fantasy of a "Jurassic Park" movie. When phylogenetic programs try to place dinosaurs in a phylogenetic “tree of life,” they must use guesses about what the DNA of dinosaurs looked like. Similar guesses must be made about almost all of the species being considered.

6. We should have little confidence in phylogenetic programs, given their extremely complicated algorithms that are anything but straightforward.

A document on molecular phylogenetics says this: “The likelihood calculations required for evolutionary trees are far from straightforward and usually require complex computations that must allow for all possible unobserved sequences at the LCA nodes of hypothesized trees.” The same document shows an equation for calculating likelihood, the type of equation used by such a program. It looks as complicated as one of the more complicated equations used in Einstein's theory of general relativity. See here to look at  some of the extremely complicated math involved.

When computer programs are based on extremely complicated algorithms, there will very often be bugs in the program – either because of an error in the complicated algorithm or because of a failure in accurately translating the complicated algorithm into computer code such as Java. For example, a recent study found bugs in software used to analyze brain scans, and estimated that thousands of scientific studies using such software may be inaccurate. The more complicated an algorithm, the greater the likelihood it will not be accurately implemented in bug-free computer code.

A paper entitled “The State of Software in Evolutionary Biology” reviewed various computer programs used in phylogenetics, and concluded “the software quality of the tools we analyzed is rather mediocre.” A later paper entitled "The State of Software for Evolutionary Biology" stated, "The software engineering quality of the tools we analyzed is rather unsatisfying." It is a huge problem in science that software programs used for scientific analysis are often written by scientists who dabble in computer programming, and the quality of their work is often second-rate.  We should no more expect high-quality code from a scientist dabbling in computer programming than we should expect to get high-quality house-building and plumbing from a professional musician who dabbles in making houses. 

7. We should have little confidence in phylogenetic programs, because there is no way to test the output of such programs.

As a general rule, our confidence in a type of software should be proportional to the degree to which the software has passed tests. For example, if some baseball prediction software were to predict that a particular player would have a batting average next season of .314, and the player did produce exactly such a batting average, and the same type of prediction succeeded for other players, that would be a good sign that the software was reliable. But in the case of phylogenetic software, there is no way to test its outputs. Although certain types of consistency checks and statistical checks can be applied to the output of phylogenetic software, we have no way of verifying that a "tree of life" or an inheritance tree produced by such software is historically accurate. Anyone in the software industry knows that untested software is not something you should have much confidence in.

8. Lateral gene transfers cast doubt on the reliability of  phylogenetic estimates.

Here is a quote from a 2016 scientific paper:

One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to “uproot the Tree of Life (TOL)” [1]. Lateral gene transfer (LGT) is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain.

The paper then goes on to say this:

Students of animals and plants have long accepted that incomplete lineage sorting, introgression, and full-species hybridization pose difficulties for the sorts of trees that Darwin might have had us draw. But it is microbes, with their promiscuous willingness to exchange genes between widely separated branches of any “tree,” that have most seriously jeopardized the neo-Darwinian synthesis.

9. Disagreement about mutation rates undermines the reliability of phylogenetic estimates.

The output of a phylogenetic program may rely on some estimate regarding a rate of mutation. But there is great disagreement about the rate of mutation in the past. A scientist quoted in Nature News says this about the “DNA clock” used in phylogenetics:

The fact that the clock is so uncertain is very problematic for us,” he says. “It means that the dates we get out of genetics are really quite embarrassingly bad and uncertain.”

10. Phylogenetic estimates based on microRNAs or fossils conflict with other phylogenetic estimates.

The quote below is from a 2012 article published in the mainstream publication Nature:

A molecular palaeobiologist at nearby Dartmouth College, Peterson has been reshaping phylogenetic trees for the past few years, ever since he pioneered a technique that uses short molecules called microRNAs to work out evolutionary branchings. He has now sketched out a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents. “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. The technique “just changes everything about our understanding of mammal evolution.”
The mainstream scientific paper "How reliable are human phylogenetic hypotheses?" gives a troubling answer to such a question.  It tells us that "phylogenetic hypotheses regarding humans and their fossil relatives" have "never been subjected to external validation." When the authors tried to do such a validation, they found that "phylogenetic hypotheses based on the craniodental data were incompatible with the molecular phylogenies."   This led them to conclude that "existing phylogenetic hypotheses about human evolution are unlikely to be reliable." 

Below is a visual from a 2016 paper "A new view of the tree of life." In this paper this visual comes underneath a headline "A current view of the tree of life."  You may notice that the strange shape has no actual resemblance to a tree, although it looks a little like some erupting fireworks sparkler stick that I would use as a young boy on the fourth of July.  

No doubt computational phylogenetics will continue to be very popular. Although such analysis seems to add little to our knowledge, it's a nice easy way to make a living if you are an evolutionary biologist. Rather than having to do the messy and frustrating work of trying to dig up fossils, an evolutionary biologist can just comfortably sit in an office and crunch genome data. It's a lot easier than writing software, where there is typically the requirement that your computer work must actually achieve some useful innovation. A scientist specializing in phylogenetics can just grind out hypothetical “trees of life” or “ancestry trees” year after year, with very little disturbance from people objecting to his work or analyzing his methods. So if you are an evolutionary biologist making a living doing such comfortable work in a clean office, you will vigorously defend the value of what you are doing. The last thing you want is to have to go out in the mud and get your fingernails dirty.

Saturday, January 26, 2019

The Two Kings: A Science Fiction Story

On an extraterrestrial planet far away, a planet revolving around a distant star, young Tyroc was excited. For the first time, the young prince was going to play with another prince, and it was a boy almost the same age as him.

His father the king introduced the young boy to Tyroc. “This is Maldred,” said the king. “Like you, he is the prince of a small country. I’m sure you two kids will have fun playing together.”

The two children played together in a room filled with expensive toys. Maldred looked at the toys, and was immediately attracted to the toy soldiers and war planes. “Let’s play war!” said Maldred. “I’ll be the attacker, and you can be the defender.”

I don’t really like playing war,” said Tyroc. “My father got me those war toys, but I don’t use them very often. What I really like to play with is blocks. I like to arrange the blocks into big fancy buildings.”

For about 30 minutes Maldred played with the toy soldiers and war toys, while Tyroc built from the wooden blocks a tall fancy building, which reached 3 feet high. Finally Maldred held a big toy plane in his hand, and yelled, “Incoming bomber!” He swooped in the plane, smashing it into the building Tyroc had created, toppling all the wooden blocks to the ground.

Tyroc thought this was very rude, but he tried not to get too upset about it.

Seventeen Years Later

When Tyroc was 25, his father died. Tyroc became the king of his small country. He had enormous riches he could use, but he didn’t have to concern himself with running his small country, which was a constitutional monarchy. Most of the government decisions were made by the ruling congress of his small country. A year later Maldred’s father died, and Maldred became the king of his country. Unlike Tyroc, Maldred had absolute power in his country. He was the dictator of his land.

The two kings began following very different paths.

Tyroc was very interested in architecture. He wanted to create buildings, and design new cities. He conceived grand ideas about fantastic cities that he could build, and began drawing up plans for these projects.

His first great project was the creation of a city on a mountain top. In Tyroc’s land there was a very tall mountain with a large flat top a mile wide. Tyroc thought it would be wonderful to create a small city on top of this mountain. It would look like nothing else that existed in the world. He designed all the buildings, and had his royal builders build them. When it was done, he named this fantastic creation Mountaintop City.

When this was done, his exhausted royal builders said, “Well, I hope we won’t have to do anything that hard for a long time.”  “Are you kidding?" replied King Tyroc. "I have lots of other ideas for fantastic cities I want to create!”

Far away, in the land he ruled over, King Maldred concentrated on waging war. He built up his armies into a fearsome force, and invaded the country to the south. He began to fight battles with great intensity, shedding much blood.

Four Years Later

King Tyroc’s next project was the creation of a city that he called Castle City. It was a most unusual and beautiful city, because every building in it was a castle. Even the shopping malls and office buildings and supermarkets were all castles.

The royal builders complained that King Tyroc’s projects were going to bankrupt the royal treasury. But as soon as the Castle City was finished, people from all over the world flocked to visit it. This made vast amounts of additional money for the royal treasury. King Tyroc soon began to plan other amazing cities to create.

One day King Maldred came to visit King Tyroc. “Old friend, I’m having such fun with my wars and conquests. You must join me in my battles, and add your forces to my invading armies.” But King Tyroc wasn’t interested. “No, I’d rather not,” he said. “I have more building projects that I am very busy with.” Disappointed, King Maldred left.

Six Years Later

King Tyroc next asked himself, “What other city can I create – one like no other city that exists?” Finally he came up with an astonishing idea: the idea of creating a floating city. In his land there was a large lake with the deepest blue water, which had been formed by a volcano that exploded long ago. King Tyroc’s idea was to place a floating city in the middle of this lake. His royal builders told him he was crazy, that it would never work. But finally, after some trial and error, he figured out exactly how to make the floating buildings.

The city he created, floating in the middle of the deep blue lake,  was like nothing his planet had ever seen. Tourists flocked to see it, which refilled the royal treasury, giving more funds for King Tyroc’s next project.

Meanwhile the fierce King Maldred continued to raise more armies, and invade more countries.

Five Years Later

King Tyroc had thought long and hard about what building project he should work on next. Finally he came up with his most ambitious idea: a city that would be called the Domed City. It would be a city surrounded by a gigantic gleaming glass dome, a mile high. Inside the city there would be no need for umbrellas, and the temperature would always be 70 degrees.

His royal builders thought he was crazy. But finally, working with many engineers and scientists, he found a way to create this amazing city. When it was finished, some people said it was the most amazing and beautiful city in the world. The tourists came from all corners of the globe to see it, and this refilled the royal treasury, again giving King Tyroc more money for new building projects.

King Tyroc began to think of ideas for other fantastic cites he could create, such as a Crystal City and an Underwater City.

Thirty Years Later

King Tyroc and King Maldred met one last time, when they were both old men.

King Maldred talked all about his many conquests, wars, and battles. He told of the many times he had pounded his enemies into submission, and had crushed his foes without mercy.

King Tyroc preferred to talk about the amazing cities he had built. He showed King Maldred pictures of all the unique and remarkable buildings he had designed and built. “All together, I have built seven cities,” said King Tyroc proudly.

Why that’s a coincidence,” chuckled King Maldred. “You’ve BUILT seven cities, and in all my wars and battles and conquests, I’ve DESTROYED seven cities. Ha ha ha ha ha!”

King Maldred thought this little coincidence was very funny, and he laughed about it heartily for ten seconds. King Tyroc looked sadly at King Maldred, and walked away without saying anything. King Maldred was left alone in the room. For some reason he began to feel ill at ease, and started to frown.

Within a few years, both kings died.

After his death the deeds of King Maldred were quickly forgotten. This is because the blood-stained pages of his planet's history were very crowded with the deeds of fierce war-makers, and King Maldred had not done anything to distinguish himself from the others of his type. But the deeds of King Tyroc were never  forgotten. He had earned himself a lasting place in the memory of his people. For centuries that followed, people remembered King Tyroc and his amazing creations, and thought about him whenever they visited his cities. And history gave a name to this king, who was known and remembered throughout his planet as King Tyroc the Builder.

Wednesday, January 23, 2019

When Minds Seem to Borrow Bodies

There are many different types of evidence for paranormal phenomena. They include the following:

  • Near-death experiences (reports of inexplicable events experienced by people who had a close encounter with death, but who survived)
  • Deathbed visions (reports of visions of dead relatives or a world beyond by people who did die soon after making such reports), such as reported by Barrett and as reported by Osis and Haraldsson 
  • Apparition sightings such as those abundantly reported in Chapter 3 of the superb book The Unknown by Flammarion, one of the most well-known astronomers of his day, and also very abundantly documented by the massive work Phantasms of the Living
  • Laboratory tests of extrasensory perception, such as the convincing evidence gathered at universities by professors such as Rhine and Riess
  • Incidental accounts of extrasensory perception, which are quite commonly reported (you can find many examples here in Chapter 6 of The Unknown by Flammarion, and also in the book The Gift
  • Inexplicable physical manifestations (such as materializations) occurring near mediums or during seances 
  • Cases of people who seem to receive literary content through "automatic writing" or Ouija boards, the most interesting one being that of Pearl Curran, who (despite a lack of a high-school education) produced some very high quality literary works in such a way, works displaying a mastery of language we would expect only a college graduate to have
  • Inexplicable information retrievals occurring during sessions with mediums (such as the case of Leonora Piper)
  • Cases of children who report living past lives, such as the cases very well documented by Ian Stevenson
  • Cases of people who are hypnotically regressed, and report past lives
  • Evidence for remote viewing, which was gathered by the US government, which funded remote research for many years, mainly because it seemed to be producing inexplicable results
  • Photographs of mysterious orbs, including my photographs of 500+ striped orbs which often have strongly repeating patterns, and my photos of 700+ speeding orbs
  • The "Global Consciousness Effect," a six-sigma effect in random number generators (relating to historical events) described here and here
  • Cases of apparent spiritual possession, in which one person's body seemed to be possessed by the mind or spirit of a different person

Let's take a look at the last of these items. In the literature of paranormal phenomena, there are countless cases of mediums or "channelers" who seemed to briefly go into a trance state or an abnormal mental state,  and then spoke as if some other mind had borrowed their body.  I speak here of cases in which a person's body rather appears to be borrowed for a relatively brief time, such as a number of minutes or a few hours. Such an apparent "borrower" of the person's body may be identified as a "spirit control." In some cases the person may start speaking as if he or she is a particular deceased historical person, or some unknown figure.  A fascinating example was the case of Jane Roberts, who would often seem to be possessed by a mind identified as Seth. Several interesting books (sometimes called the Seth Material) were compiled from the utterances of this "Seth" personality that seemed to borrow Roberts' body. 

Another similar case was that of the Brazilian healer Arigo, who would very often act as if he was possessed by the spirit of a German doctor. Speaking in a heavy German accent at such times, Arigo (who lacked medical training) apparently performed countless cures and successful surgical operations. 

What is much less common are cases in which a person's mind and personality seems to vanish for many days, apparently to be replaced by the mind of a deceased person. One occurred in the US, and another in India. Neither was reported as a case of demonic possession, meaning both cases were free from the intellectual baggage associated with that idea.

The case in the US was the case reported in the book “The Wasekea Wonder” written by E.W. Stevens, and published in 1878. You can read the original account at this location. The account describes events that occurred in Watseka, Illinois in 1877 and 1878. In a case like this, the fact that we can read a contemporaneous account written soon after the events is a fact bolstering the credibility of the evidence.

My description will be drawn purely from Stevens' original 1878 account. On page 1 of the Stevens account we are told that Mary Lurancy Vennum was born April 16, 1864 to Thomas and Lurinda Vennum. The Vennum family moved to Waseka, Illinois in 1871, locating “40 rods” (about 200 meters) from the residence of A.B. Roff. Page 1 tells us the following:

The only acquaintance ever had been between the two families during the season, was simply one brief call of Mrs. Roff, for a few minutes, on Mrs. Vennum, which call was never returned; and a formal speaking acquaintance between the two gentlemen. Since 1871, the Vennum family had lived entirely away from the vicinity of Mr. Roff's, and never nearer than now, on extreme opposite limits of the city.

From July 1877 to January 1878 Mary Lurancy Vennum had various bizarre sicknesses and trances, claiming to see heaven, angels and spirits. On February 1, 1878, Mary's father reported something astonishing (according to page 4 of the Stevens account):

On the following morning, Friday, February first, Mr. Vennum called at the office of Mr. Roff and informed him that the girl claimed to be Mary Roff and wanted to go home. To use Mr. Vennum's wards: “She seems like a child real homesick, wanting to see her pa and ma and her brothers."

Who was this Mary Roff? On page 4 of the Stevens account, we are told that Mary Roff, the daughter of Asa and Ann Roff, was born on the eighth day of October, 1846, in Indiana. On page 6 we are told that Mary Roff died on July 5, 1865, the year after the year that Mary Lurancy Vennum was born. So when Mary Lurancy Vennum claimed to be Mary Roff in February, 1878, she was claiming to be someone who had died 13 years ago.

On page 6 of the Stevens account, we are told the following:

About a week after she took control of the body, Mrs. A. B. Roff and her daughter, Mrs. Minerva Alter, Mary's sister, hearing of the remarkable change, went to see the girl. As they came in sight, far down the street, Mary, looking out of the window, exclaimed exultingly, "There comes my ma and sister Nervie!" the name by which Mary used to call Mrs. Alter in girlhood. As they came into the house, she caught them around the necks, wept and cried for joy, and seemed so happy to meet them. From this time on she seemed more homesick than before. At times she seemed almost frantic to go home.

On page 7 Stevens tells us that the following happened a few days later:

On the eleventh day of February, 1878, they sent the girl to Mr. Roff's, where she met her “pa and ma," and each member of the family, with the most gratifying expressions of love and affection, by words and embraces. On being asked how long she would stay, she said, "The angels will let me stay till sometime in May;" and she made it her home there till May twenty-first three months and ten days, a happy contented daughter and sister in a borrowed body.

For three months the teenager with the body of Mary Lurancy Vennum acted just like the deceased Mary Roff, and as if she no longer had the mind of Mary Lurancy Vennum. Referring to the Roff home, and using the phrase “everything that Mary knew” to refer to everything that Mary Roff knew, the Stevens account on page 7 tells us this about the teenager:

The girl now in her new home, seemed perfectly happy and content, knowing every person and everything that Mary knew when in her original body, twelve years to twenty-five years ago, recognizing and calling by name those who were friends and neighbors of the family from 1852 to 1865, when Mary died, calling attention to scores, yes, hundreds of incidents that transpired during her natural life. During all the period of her sojourn at Mr. Roff's she had no knowledge of, and did not recognize any of Mr. Vennum's family or neighbors, yet Mr. and Mrs. Vennum and their children visited her and Mr. Roff's people, she being introduced to them as to any strangers.

On page 8 Stevens says that Mr. Roff (the father of the deceased Mary Roff) wrote him on February 19, 1878, about three weeks after the apparent “mind switch,” saying the following (referring to Mary Lurancy Vennum):

Mary is perfectly happy; she recognizes everybody and everything that she knew when in her body twelve or more years ago. She knows nobody nor anything whatever that is known by Lurancy.

After some three months, there seemed to occur strange oscillations in which the body of Mary Lurancy Vennum seemed to switch between the mind or soul of Mary Roff and the mind or soul of Mary Lurancy Vennum. Before returning to normal, the teenager bid a tearful farewell to Mr. Roff. Soon thereafter the astonishing “switch” was over. Now identifying herself as the original Mary Lurancy Vennum, the teenager joyously greeted her parents, like someone who had been away for the summer in a summer camp.

Mary Lurancy Vennum

Although it was called a "singularity" by one writer, the astonishing case of Mary Lurancy Vennum (the Watseka Wonder) is not unique. A distinguished researcher has documented a similar case that occurred in India.  The case is described in the paper "A Case of the Possession Type in India With Evidence of Paranormal Knowledge" by Ian Stevenson and two other researchers (Pasricha and McClean-Rice).  There is the remarkable detail that a woman named Sumitra seemed to die or fall into a coma, and then awoke claiming to be a no-longer-living person named Shiva who lived 100 kilometers away. 

Below is Stevenson's summary of the case:

A young married woman, Sumitra, in a village of northern India, apparently died and then revived. After a period of confusion she stated that she was one Shiva who had been murdered in another village. She gave enough details to permit verification of her statements, which corresponded to facts in the life of another young married woman called Shiva. Shiva had lived in a place about 100 km away, and she had died violently there-either by suicide or murder-about two months before Sumitra's apparent death and revival. Subsequently, Sumitra recognized 23 persons (in person or in photographs) known to Shiva. She also showed in several respects new behavior that accorded with Shiva's personality and attainments. For example, Shiva's family were Brahmins (high caste), whereas Sumitra's were Thakurs (second caste); after the change in her personality Sumitra showed Brahmin habits that were strange in her family. Extensive interviews with 53 informants satisfied the investigators that the families concerned had been, as they claimed, completely unknown to each other before the case developed and that Sumitra had had no normal knowledge of the people and events in Shiva's life. The authors conclude that the subject demonstrated knowledge of another person's life obtained paranormally.

The case has some interesting parallels with the Vennum case. In both cases: (1) before the reported "mind switch" the subject experienced a strange sickness that included one or more trances; (2) in both cases the subject suddenly reported that she was now a different person who had died; (3) in both cases the subject was able to make numerous identifications that should have been possible only for the person who died; (4) in both cases at the same time the subject claimed to be the person who had died, she no longer recognized family members belonging to her original family (not the family of the person who previously died); (5) in both cases the "spiritual possession" seemed to last for more than two months. Both cases were written up in the same year they occurred, and the Stevenson 1989 paper was partially based on a 1985 newspaper account published in the same year as Sumitra's "mind switch" to that of the deceased woman named Shiva. 

While Mary Lurancy Vennum spent only three months claiming to be the late Mary Roff, before assuming her original personality, in the case of Sumitra she seemed to have the mind of the deceased Shiva for more than two years. 

The Sumitra case is perhaps even better as evidence than the Mary Lurancy Vennum case. The family of Mary Roff had a slight interaction with the family of Mary Lurancy Vennum (but without conversation between the one Mary who died a year after the other Mary was born), prior to the alleged "mind switch" in which Mary Lurancy Vennum started acting like Mary Roff. But prior to the time that Sumitra started acting like Shiva, there was no interaction between Sumitra or her family and Shiva or her family, who lived 100 kilometers away.  In 1985 there was no Internet allowing anyone to find out details about someone living 100 kilometers away.  The Stevenson paper reported that Sumitra was able to make 12 identifications of Shiva's family members and friends under conditions which "excluded cueing."  

Both the Mary Lurancy Vennum case and the Sumitra case were written up by medical professionals who thoroughly interviewed the persons interacting with the case not long after the events occurred. For example, Stevenson's co-author Satwant Pasricha (a clinical psychologist) interviewed some members of the family of Sumitra and Shiva in 1985, the same year Sumitra's "spiritual possession" began; and Stevenson (a professor of medicine and psychiatry) and his co-authors interviewed 24 members of the family of Sumitra and the family of Shiva in 1986 and 1987.  The Mary Lurancy Vennum case was documented by a physician (Stevens) who interviewed the relevant persons in the same year the events occurred.  In both cases, every fact documented seemed to support the astonishing hypothesis of a body being long borrowed by another mind, the mind of a real person who had died. 

Postscript: I have found one other case similar to the cases described above: the case of Uttara Huddar, an Indian woman described below by an entry in the Psi Encyclopedia of the Society for Psychical Research:

"This is a 1970s Indian case of an educated woman, Uttara Huddar, whose personality and memories abruptly changed at the age of 32 to those of a rural villager, Sharada, who had lived and died a century and a half earlier. The transformation proved temporary, but the Sharada personality continued to appear intermittently throughout Uttara’s life. A striking feature of this case is the linguistic element: as ‘Sharada’, Uttara was unable to speak Marathi, her native language, only Bengali, which she previously knew only a little, but could now speak fluently, and in an archaic dialect."

You can read about this fascinating case here

Saturday, January 19, 2019

The Myths and Mystery of Morphogenesis

For decades scientists and science writers have been pushing the false claim that DNA is some kind of blueprint or recipe for making an organism. But in the mainstream science magazine Nautilus a scientist has “fessed up” in great detail that this idea is bunk. The confession is in a long post entitled “It's the End of the Gene As We Know It,” by biologist Ken Richardson.

Richardson quotes physicist Erwin Schrodinger as saying this in 1943 about the chromosomes: that they “contain, in some kind of code-script, the entire pattern of the individual’s future development and of its functioning in the mature state.” In 1943 this idea was purely a speculation. But in a few years DNA was discovered, and some claimed that Schrodinger's idea had been confirmed. 

DNA does contain a code-script of a sort, and it uses a system called the genetic code in which chemicals in DNA (called nucleotide base pairs) stand for amino acids that make up proteins. But under such a system there is only a very limited capacity for specification. DNA (and the genes that make up DNA) can only specify the amino acids that make up proteins, and the contents of RNA molecules. When scientists discovered the genetic code used by DNA, they only discovered an extremely limited “poor man's language” completely incapable of specifying complex three-dimensional structures such as the layout of a human body or the structure of an eye or the layout of the human reproductive system. 

We can compare the genetic code used by DNA to a tiny little “sandwich language” in which the only words are the names of sandwich ingredients: words such as “bread,” “tomato,” "salami," “cheese,” and “ham.” With such a tiny little language, you can specify any number of sandwiches, but you can't specify something like the anatomy of an eye or the anatomy of a mammal. Similarly, with its “poor man's language,” DNA can specify the linear arrangement of amino acids in a protein, and the contents of RNA molecules, but that's about it.

Completely ignoring the inherent physical limitations of DNA, scientists and scientific writers have for seventy years been peddling what I call the Great DNA Myth. It is the myth that DNA (and the genes in it) are a blueprint or a recipe or a program for making an organism. Describing how this myth has been told, and suggesting a counter-trend, Richardson states the following:

In scientific, as well as popular descriptions today, genes 'act,' 'behave,' 'direct,' “control,' 'design,' 'influence,' have 'effects,' are “responsible for,' are 'selfish,' and so on, as if minds of their own with designs and intentions. But at the same time, a counter-narrative is building, not from the media but from inside science itself.”

Shortly after saying this Richardson states the following, negating the very claims that he has just assured us are so widespread:

"Scientists now understand that the information in the DNA code can only serve as a template for a protein. It cannot possibly serve as instructions for the more complex task of putting the proteins together into a fully functioning being, no more than the characters on a typewriter can produce a story."

Richardson is correct in what he has said about DNA, which cannot be a blueprint or a specification for the body plan of an organism. But he has left us with a glaring inconsistency between what he says “scientists now understand” and what he has previously stated that scientists are saying, making it sound as if scientists are feeding us bunk that is inconsistent with what they understand.

Richardson approvingly quotes biologist Denis Noble as saying, “DNA is not a cause in an active sense” and that DNA “is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.” This is correct, and if we think of DNA as mainly a chemical ingredient list we will be getting on the right track. Ingredient lists don't cause things to be built, and don't contain either blueprints or recipes for making complex visible structures. A recipe always includes assembly instructions that go beyond an ingredient list. “Three eggs” is not a recipe for making a three-egg omelet.

Richardson tells us some things that contradict the “DNA is a blueprint” dogma. He tells us, “Increasingly, we are finding that, in complex evolved traits—like human minds—there is little prediction from DNA variation through development to individual differences.” Contradicting the idea that DNA specifies an organism, Richardson states the following:

"Conversely, it is now well known that a group of genetically identical individuals, reared in identical environments—as in pure-bred laboratory animals—do not become identical adults. Rather, they develop to exhibit the full range of bodily and functional variations found in normal, genetically-variable, groups. In a report in Science in 2013, Julia Fruend and colleagues observed this effect in differences in developing brain structures."

Richardson tries to make it sound as if the idea that DNA or genes are a blueprint or recipe for making a human is an idea that is mainly discredited by recent developments in the past few decades. Such a narrative is rather a half-truth. It is certainly true that some things that have occurred in the past few decades have strongly discredited the idea that DNA is a blueprint or recipe for making a human. Some of these things have been: (1) the complete failure of massive DNA analysis projects such as the Human Genome Project and the ENCODE project to find in DNA or genes any such thing as a blueprint or recipe for making a human or any organ of a human or even any cell of a human; (2) the discovery (to quote Richardson) that “there is no correlation between the complexity of living things and the number of genes they have,” and that organisms such as a simple rice plant have twice as many genes as humans.

But there is a reason why it is a half-truth to make it sound as if the idea that DNA or genes are a blueprint or recipe for making a human is an idea that is mainly discredited by recent developments in the past few decades. The reason is that extremely strong reasons for rejecting this idea have existed for about seventy years, since the time of the discovery of DNA. The first such reason is that the genetic code used by DNA only allows for proteins or RNA to be specified, and is completely insufficient for stating complex three dimensional structural information such as how to construct a human being. The second such reason is that there does not exist anything in the human body capable of interpreting such instructions if they happened to exist in DNA. Very complex instructions require a very complex instruction reader, and there is no such thing in the womb of a human body. If DNA happened to have the incredibly complex instructions needed to build a human, there would be nothing in a womb capable of reading instructions so complex and executing them.

So from the time DNA was discovered, there were the strongest reasons reasons for rejecting the whole “DNA is a blueprint for a human” idea. So why was such an idea taught so many times? It's because it was a pillar of Neo-Darwinism, the “modern synthesis” which attempts to explain the origin of biological innovations by saying they occurred entirely because of changes in genomes (that is, changes in DNA). When we have a proper idea, that DNA is merely a chemical database, the legs are pulled out from under the table of Neo-Darwinism. Richardson quotes biologist Denis Noble as saying this about Neo-Darwinism (which is also called “the modern synthesis”): “The modern synthesis has got causality in biology wrong.”

The full quote by Noble (from this interview) is as follows:

"I think that as a gene-centric view of evolution, the modern synthesis has got causality in biology wrong. Genes, after all, if they’re defined as DNA sequences, are purely passive. DNA on its own does absolutely nothing until activated by the rest of the system through transcription factors, markers of one kind or another, interactions with the proteins. So on its own, DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires."

Shockingly, in the same interview, this distinguished biologist refers to speciation (the origin of a new species), and says, "So I go along with the view that there has been no really clear proof that speciation occurred via gradual mutation followed by selection." Here we have an admission that the central dogma of modern Darwinism has "no really clear proof." Noble here mirrors what was stated in the book Evolution and Ecology: The Pace of Life by Cambridge University biology professor K. D. Bennett. Bennett says on page 175, "Natural selection has been shown to have occurred (for example, among populations of Darwin's finches), but there is no evidence that it accumulates over longer periods of time to produce speciation in the Darwinian sense." 

Once we correctly realize that DNA cannot be a specification for a human, and does not store a human body plan, the question that immediately comes to mind: where is it that the human body plan comes from? Richardson gives us some biological double-talk to try to explain this, but his explanation makes no sense at all.

Here is what Richardson says about the process of human development:

"Within hours, the fertilized egg becomes a ball of identical cells—all with the same genome, of course. But the cells are already talking to each other with storms of chemical signals. Through the statistical patterns within the storms, instructions are, again, created de novo. The cells, all with the same genes, multiply into hundreds of starkly different types, moving in a glorious ballet to find just the right places at the right times. That could not have been specified in the fixed linear strings of DNA. So it has been dawning on us is that there is no prior plan or blueprint for development: Instructions are created on the hoof, far more intelligently than is possible from dumb DNA."

Richardson is right that this miracle of organization cannot be explained by the "bad old myth" of a DNA blueprint that causes a baby to form form an egg (for DNA is not like a blueprint, and blueprints don't build things).  But Richardson is not credible at all in asserting that “there is no prior plan or blueprint” behind morphogenesis and embryonic development. Claiming that human beings arise from “statistical patterns” that create instructions “on the hoof” is a new myth no more credible than the old myth that babies appear from a fertilized ovum because the womb is reading a DNA blueprint. A much better thing to say is that there must be some human specification or body plan, and that we do not know where it exists, or how it is used so that a full-grown baby grows from a fertilized egg.

Inexplicable by any reductionist or "bottom-up" explanation, the development of a human body from a fertilized egg strongly suggests that there is some unfathomable "top-down" effect causing biological organisms to assume their forms -- some gigantic facet of reality beyond our ken.  As for the idea that  instructions created "on the hoof" (an expression meaning "without thought or preparation") might act "far more intelligently," that makes no sense whatsoever.  Instructions created "on the hoof" by mindless chemical units would be random nonsense, not something "far more intelligent."

A recent Science Daily article reveals that scientists have not actually observed any chemical or biological instructions giving rise to the tissues and organs in a body, contrary to what Richardson has insinuated. The article states, "As cells divide to form tissues and organs in multicell organisms, they move to where they belong, informed by a series of cues that scientists have yet to observe or fully understand."  Notice the phrase "have yet to observe" in that sentence. 

To try to explain his bad new myth of morphogenesis,  Richardson uses analogies which don't make any sense in the context of his account. He compares cells that billions of times move in just the right way at just the right time to a "glorious ballet."  But ballet dancers don't produce a glorious ballet like The Nutcracker by "talking to each other" during their dance, or free-wheeling it in some spontaneous "on the hoof" manner;  they follow the instructions of a choreographer who has planned out their dances. Richardson also suggests the analogy of an orchestra working without a conductor. That analogy does not fit his claims, as orchestras work from sheet music previously designed by a composer.  A symphony orchestra in which musicians are playing their instruments "on the hoof" would produce just noise, not an organized symphony. 

They aren't winging it

Trying to explain a hundred biological wonders like the extremely intricate functional anatomy and biochemistry of the eye by citing "statistical patterns" is rather amusing.  Evoking "statistical patterns" to explain something is the kind of empty bluff people use when they don't have an explanation for something, as illustrated in the conversation below.

Jim: Why did Trump win the 2016 election?
Dave: That was just statistical patterns.
Jim: And why did the stock market crash in 2008?
Dave: That was also just statistical patterns.
Jim: And how do such beautiful spiral galaxies form in space?
Dave: Once again, statistical patterns explain it.
Jim: And why do really bad wars start up a few times in a lifetime?
Dave: Again, it's just statistical patterns.
Jim: Why, Dave you're a genius! You can explain almost anything.

I may note that Richardson does a rather poor job of accounting for the lineage of his “DNA cannot be a blueprint or recipe” assertions. He rather makes it sound as if such a thing is a fairly recent development. But the transparent absurdity of claiming that DNA is a recipe or blueprint or program has long been pointed out by various critics of biological orthodoxy. The idea that DNA is not a blueprint or recipe or program for making a human, and cannot account for human development, was forcefully argued at length in my February 2016 post “The Gigantic Missing Link of Biological Life.” But a much earlier statement of the idea can be found in a 1987 paper by contrarian biologist Rupert Sheldrake, who stated the following:

"DNA only codes for the materials from which the body is constructed: the enzymes, the structural proteins, and so forth. There is no evidence that it also codes for the plan, the form, the morphology of the body. To see this more clearly, think of your arms and legs. The form of the arms and legs is different; it's obvious that they have a different shape from each other. Yet the chemicals in the arms and legs are identical. The muscles are the same, the nerve cells are the same, the skin cells are the same, and the DNA is the same in all the cells of the arms and legs. In fact, the DNA is the same in all the cells of the body. DNA alone cannot explain the difference in form; something else is necessary to explain form."

Sheldrake attempts to account for morphogenesis and embryonic development by speculating that there is a gigantic facet of reality overlooked by humans, something he calls morphic resonance.  He seems to imagine morphic resonance as some natural reality outside of a human body where the body plan is stored. That may or may not be the right explanation. But I think Sheldrake is on the right track in assuming that we can only account for the development of a human baby from a fertilized egg by postulating some gigantic additional reality beyond the human body to account for such an effect. 

When a child has learned how a human egg is fertilized through sexual intercourse,  people say that such a child has learned how babies originate. But the child has not actually learned such a thing.  For neither any children nor any adults can actually explain how babies originate in the sense of explaining how a fertilized egg is able to progress to become a baby.  

Nearly a century ago, the physician Gustave Geley stated that the facts of morphogenesis and embryonic development force upon us the idea that biological changes in an organism must come from some directing exterior force or "dynamism" outside of the body. He stated the following:

"In order to understand all these—the mystery of
specific form, embryonic and post-embryonic development,
the constitution and maintenance of the personality,
organic repair, and all the other general problems of
biology—it is necessary and sufficient to accept a notion,
which is certainly not new, but is placed in a new light,
the notion of a dynamism superior to the organism and
conditioning it....This is a concrete idea —that of a directing and centralizing dynamism, dominating both intrinsic and extrinsic contingencies, thchemical reactions of the organic medium, and the influences of the external environment."

Nothing we have learned in the many decades since these words were written makes the idea obsolete, and the concept still seems as necessary as when Geley suggested it, because chemistry within a developing body is utterly insufficient to explain the morphological progression of that body from an egg to an adult. 

We take for granted the miracle of morphogenesis simply because we observe it happening invariably.  It's a rather a rule that anything that is observed invariably occurring will always be taken for granted, no matter how inexplicable or seemingly providential such a thing may be. Let us imagine a strange planet on which there are many volcanoes. But let us suppose that on this odd planet instead of volcanoes ejecting rocks and lava randomly all over the place, volcanoes only eject rocks and lava that conveniently form into habitable houses, some multi-storied.  On such a planet the scientists would probably regard such a thing as just being a "law of nature" rather than some wonderful blessing.  On that planet we might hear conversations like this:

Professor: So when volcanoes erupt, they shoot out lava and rocks that always conveniently form into habitable houses and buildings. We call this law of nature "the law of convenient volcanoes." 
Pupil: My father says that such a law is a sign of some purposeful intelligence working for our behalf. 
Professor: Superstitious nonsense! The "law of convenient volcanoes" is simply the way blind nature has always worked. No doubt such a law of nature prevails on all inhabited planets. 

Similarly, today's earthly scientists, who have no real explanation for how a human progresses from an egg to an adult, typically assume that a similar wonder occurs on many other planets to produce full-grown extraterrestrial beings. 

Tuesday, January 15, 2019

Closed Minds of a Professorial Priesthood

It is very widely acknowledged that one of the traits of a good scientist is open-mindedness. Open-mindedness can be described as the ability to concede that your idea about how something works may be wrong, and a tendency to objectively weigh any evidence that comes up suggesting that the thing may have an explanation or characteristics very different from what you normally think. Almost all of today's scientists would describe themselves as having the virtue of open-mindedness. But the truth is that a large fraction of them are not very open-minded at all. The problem is that scientists are created by university belief enclaves that are breeding grounds for closed-mindedness.

Graduate programs for scientist training may be compared to the seminary education by which people become priests. To become a Catholic priest you must send four years studying in a seminary, and then spend one year as a transitional deacon. To get a PhD in some branch of science, you must spend four or more years in some graduate program, and often as long as seven years or more. A Catholic seminary is an ideological enclave in which all the instructors share a very specific dogmatic belief system. Many a university graduate program is also an ideological enclave in which all the instructors share a very specific dogmatic belief system.

At a Catholic seminary you are taught to unquestioningly accept dogmas such as the Trinity, the physical resurrection of Jesus, and papal infallibility. At a university graduate program you may be taught to unquestioningly accept dogmas such as the dogma that life appeared through chance combinations of chemicals, the dogma that random mutations and natural selection caused the origin of each species, the dogma that brains produce minds, the dogma that synapses store memories, and the dogma that no can have any special psychic powers or psychic experiences beyond the explanation of neuroscientists.

An unwritten rule of many an exclusive social group is what we call the principle of “make it hard to enter the group.” If you make it so that a person must spend hard years to enter some group, you will maximize the chance that people entering that group will conform to its norms once they go to all the trouble of getting into the group. I once saw a fascinating documentary that showed how this “make it hard to enter the group” principle was used by a motorcycle gang. The gang had the rule that to enter as a new member of their motorcycle gang, you first had to spend years doing lowly favors for the gang members, such as fetching them drinks and food. This way the gang made sure that the only people who got into the gang were those willing to pay a high price in effort to enter it; and such people would be very likely to conform to the group's norms once they had gone to such trouble to get into the group.

Seminaries and graduate programs also make use of this “make it hard to enter the group” principle. In fact, a scientist graduate school seems to use such a principle to a much greater degree than a seminary. A typical seminary student doesn't have to pay for his education, but a person studying for a PhD typically has to invest a huge amount in tuition and other university fees, which could easily be $100,000 or more. Just as it is very unlikely someone will spend four hard years of time in seminary education to become a Catholic priest and then defy the belief system of that priesthood, it is very unlikely someone will invest four to eight years of time (and $100,000 or more in tuition and fees) to become a PhD, and then defy the belief norms of the scientist group he has worked so hard to get into. The person who emerges with a PhD from such long years of indoctrination may be no more likely to be open-minded about topics such as human origins, the mind-brain relation and paranormal phenomena than a newly minted Catholic priest will be likely to be open-minded on theological topics.

science dogma

A good system of scientist education is one that would train scientists to be very humble, and to recognize that their knowledge of nature is merely fragmentary. Our system of scientist education is one that leads scientists to think they are great lords of explanation who pretty much have things figured out. And so we have a neuroscientist like Kandel ending a recent book with a chapter claiming that consciousness is the “last great mystery” of the brain, thereby overestimating his knowledge of the mind and brain by many times, and failing to recognize the countless mysteries on this topic scientists have not solved. Pretentious conceit about your level of knowledge about nature cannot co-exist with open-mindedness.

Very closed-minded scientists sometimes hypocritically lecture us on the virtue of open-mindedness. An example of this is a post on the Real Clear Science site entitled “What It Really Means to Be Open-Minded.” In that post we hear a quote from neuroscientist Steven Novella telling us it is important for scientists to be open-minded. He states the following:

"Scientists, critical thinkers, and skeptics can and should be completely open-minded, which means being open to the evidence and logic whatever it says. If the evidence supports a view, then we will accept that view in proportion to the evidence."

Such a statement of principles is very amusing coming from Novella, who over the years in his blog posts has shown himself to be an extremely closed-minded thinker who automatically rejects any evidence that seems to clash with the tenets of neuroscience orthodoxy, as reflexively as a man may jerk his knee after it is struck with a wooden hammer. An example of Novella's inappropriate closed-minded thinking is a statement he made in a blog post last year:

"Psi or anomalous cognition, is a group of alleged phenomena that include sensing what other people are thinking, viewing remote locations not accessible to the normal senses, and predicting the future in some way. These claims are inherently implausible because there is no way to account for them with known phenomena. They appear, therefore, to violate well-established laws of physics. Therefore, any reasonable scientists would argue, the threshold of evidence needed before concluding that a psi phenomenon is real should be very high. What we have is very low-grade evidence at best, therefore it is reasonable to reject claims for psi."

This is closed-minded obstinacy. The claim that the evidence for psi is “very low-grade evidence at best” is a simple falsehood. Extremely convincing laboratory experiments showing the reality of things like ESP have been done for more than a century. An example is the experiment done by professor Riess in which a person at a remote location was tested, and scored more than 70% on 1850 trials, in a test in which the expected result by chance was only 20%. The chance probability of this has been estimated  as 1 in 10 to the 700th power. The reason why the overwhelming scientific evidence for ESP has not been sufficiently accepted by scientists is that people like Novella keep telling us falsehoods by saying things such as the evidence for psi is “very low-grade evidence at best.”

Yesterday on the Psychology Today web site, we had a surprisingly good summary of the overwhelming evidence for psi, presented by Steve Taylor PhD. Taylor tells us, "The evidence for psi is already very convincing," and refers us to this recent review published in the mainstream scientific journal American Psychologist, a review which tells us, "The evidence for psi is comparable to that for established phenomena in psychology and other disciplines."  

As for Novella's reasoning about possibility and the laws of physics, they contain two glaring errors. The first is his statement, “These claims are inherently implausible because there is no way to account for them with known phenomena.” You do not show the unlikelihood of something by the fact that there is no way to account for it with known phenomena. It happens quite frequently in the course of science history that scientists make novel observations that cannot be accounted for by the explanations known at that time, leading scientists to come up with new ideas about causes. An example is how observations of stellar rotation rates around the galactic center led scientists to postulate dark matter, and the example of how meteorite falls led scientists to postulate the existence of asteroids.

A more glaring error by Novella is the conclusion that since some observations cannot be accounted for with known explanations, “They appear, therefore, to violate well-established laws of physics.” The fact that you cannot account for something with known explanations does not at all suggest that any laws of physics are being violated.

Creating a pretentious priesthood through its academic ivory towers resembling seminaries, our science education system has trained scientists to be completely closed-minded about a wide variety of things. But closed-minded scientists often fancy themselves to be open-minded. There is one good way to test whether or not a scientist is truly open-minded on a topic: look to see whether the scientist shows signs of having very carefully studied the best evidence for some idea that conflicts with the dogmatic claims made by the scientist group that scientist belongs to. If you find evidence of such erudition, it does not prove that the scientist is open-minded on the topic, but may gave you a reason to suspect that he or she is. Almost all scientists who make statements about paranormal phenomena show no signs of having spent much time studying the evidence for such phenomena.

A person may be intimidated by the thundering sounds of scientists telling us, "This is our consensus," or "We say this is impossible," as intimidated as Dorothy was when she first saw the scowling floating head of the Wizard of Oz.  But when we understand the sociological and ideological factors which often are the stilts which support such opinions, and that the pronouncements of scientists are often merely the articles of faith of a belief community, then there may occur a certain "Toto pulling back the Wizard's curtain" moment in which intimidation is reduced.