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Our future, our universe, and other weighty topics

Wednesday, November 27, 2019

Rewiring Doesn't Explain an IQ of 99 with Half a Brain

Neuroscientists have the bad habit of claiming that our minds come from our brains, and that our brains store our memories. But nature never told us such a thing. It was merely neuroscientists who told us such a thing.  When nature speaks on this topic, it often tells a tale that contradicts the dogmas that the brain makes the mind and that the brain stores memories. 

Hemispherectomy is a surgical procedure in which half of the brain is removed. The procedure can be performed on young children suffering from seizures, with surprisingly little negative impact. And the paper here also tells us on page 3 that Although most hemispherectomies are performed on young children, adults are also operated on with remarkable success.”

Very interestingly, we are told that when half of their brains are removed in these operations, “most patients, even adults, do not seem to lose their long-term memory such as episodic (autobiographic) memories.” The paper tells us that Dandy, Bell and Karnosh “stated that their patient's memory seemed unimpaired after hemispherectomy,” the removal of half of their brains. We are also told that Vining and others “were surprised by the apparent retention of memory after the removal of the left or the right hemisphere of their patients.”

On page 59 of the book The Biological Mind, the author states the following:

A group of surgeons at Johns Hopkins Medical School performed fifty-eight hemispherectomy operations on children over a thirty-year period. "We were awed," they wrote later of their experiences, "by the apparent retention of memory after removal of half of the brain, either half, and by the retention of the child's personality and sense of humor." 

In the paper "Neurocognitive outcome after pediatric epilepsy surgery" by Elisabeth M. S. Sherman, we have some discussion of the effects on children of temporal lobectomy (removal of the temporal lobe of the brain) and hemispherectomy, surgically removing half of their brains to stop seizures. We are told this:

"After temporal lobectomy, children show few changes in verbal or nonverbal intelligence....Cognitive levels in many children do not appear to be altered significantly by hemispherectomy. Several researchers have also noted increases in the intellectual functioning of some children following this procedure....Explanations for the lack of decline in intellectual function following hemispherectomy have not been well elucidated."

Referring to a study by Gilliam, the paper states that of 21 children who had parts of their brains removed to treat epilepsy, including 10 who had surgery to remove part of the frontal lobe, "none of the patients with extra-temporal resections had reductions in IQ post-operatively," and that two of the children with frontal lobe resections had "an increase in IQ greater than 10 points following surgery." The paper here (in Figure 4) describes IQ outcomes for 41 children who had half of their brains removed in hemispherectomy operations in Freiburg, Germany. For the vast majority of children, the IQ was about the same after the operation. The number of children who had increased IQs after the operation was greater than the number who had decreased IQs.

The paper here gives precise before and after IQ scores for more than 50 children who had half of their brains removed in a hemispherectomy operation in the United States.  For one set of 31 patients, the IQ went down by an average of only 5 points. For another set of 15 patients, the IQ went down less than 1 point. For another set of 7 patients the IQ went up by 6 points. 

It also should be remembered that brain-damaged patients taking standard IQ tests may have higher intelligence than the test score suggests.  A standard IQ test requires visual perception skill (to read the test book) and finger coordination (to fill in the right answers using a pencil). Brain damage might cause reduced finger coordination and reduced visual perception unrelated to intelligence; and such things might cause a subject to do below-average on a standard IQ test even if his intelligence is normal. 

There is a new study relating to the topic of intelligence and removal of half of the brain.  Once again, the study reports facts shockingly inconsistent with standard claims that the brain is the source of the human mind. But the press reporting on this study is feeding us a kind of "cover story" trying to explain away the shocking result.  Upon close inspection, this "cover story" falls apart. 

The study involved brain scans of six patients who had half of their brains removed.  Table S3 of the supplemental information of the study reveals that the intelligence quotients (IQ scores) of the six subjects were 84, 95, 91, 99,  96 and 80. So most of the six were fairly smart, even though half of their brains were gone.  How could this be when half of their brains were missing? 

In stories such as the story in Discover magazine, it is suggested that "brain rewiring" can explain such a thing. The story states the following:

"In a study published Tuesday in Cell Reports, scientists studied six of these patients to see how the human brain rewires itself to adapt after major surgery. After performing brain scans on the patients, the researchers found that the remaining hemisphere formed even stronger connections between different brain networks — regions that control things like walking, talking and memory —  than in healthy control subjects. And the researchers suggest that these connections enable the brain, essentially, to function as if it were still whole."

The summary above is not accurate, as it tells a story that is not true for one of the six patients, as I will explain below. This hard-to-swallow story (repeated by the New York Times) is reassuring if you wish to keep believing that the brain is the source of your mind.  The person who buys such a story can reassure himself kind of like this:

"How do people stay smart when you take out half of their brain? It's simple: the brain just rewires itself so that the half works as good as a whole. It acts kind of like a computer that reprograms itself to keep functioning like normal when you yank out half of its components."

We know of no machines ever built that have such a capability.  All brains engage in some "brain rewiring" every year, so any mental effect can always be attributed to "brain rewiring." We cannot dream of how a brain could possibly be clever enough to rewire itself to perform just as well when half of its matter was removed.   When we take a close look at the data in the study, it shows that this "brain rewiring" story does not hold up for the smartest subject in the study. 

In Table S4 of the study, we have measurements based on brain scanning, designed to show the level of connectivity in the brains of the six subjects.  Some of the six subjects have a slightly higher average connectivity score, but it's not very much higher.  The average connectivy scores for the controls with normal brains were .30 and .35.  The average connectivity scores for the six patients with half a brain were .43, .45, .35, .30, .43, and .41.  So it was merely true that the average brain connectivity score of the patients with half a brain was slightly higher than the normal controls.  And when we look at another metric (the "max" score listed at the end of Table S4), we see that all of the half-brain subjects had lower "brain connectivity" scores than the controls.  The "max" connectivy scores for the controls with normal brains were .90 and .74, but the "max" connectivity scores for the six patients with half a brain were only .57, .67, .49, .51, .63, and .62.  So the evidence for greater brain connectivity or "nicely rewired brains" after removal of half a brain is actually quite thin. 

Interestingly, the half-brain patient with the highest intelligence (labeled as HS4, with an IQ of 99) had an average brain connectivity score of only .30, which is the same as one of the group of controls with normal brains, and less than the brain connectivity of the other group of controls with normal brains.   So the smartest person with half a brain (who had an IQ of 99) did not at all have any greater brain connectivity that can explain his normal intelligence with only half a brain.  How can this subject HS4 have had a normal intelligence with only half a brain?  In this case, favorable brain rewiring or greater brain connectivity cannot explain the result.   So the "cover story" of "their brains rewired to keep them smart" falls apart. 

half brain
The half brain of subject HS4, IQ of 99, average brain wiring

The only way we can explain such results is by postulating that the human brain is not actually the source of the human mind.  If the human brain is neither the source of the human mind nor the storage place of memories, we should not find any of the results mentioned in this post to be surprising. 

Subject HS4 is not by any means the most remarkable case of a patient with half a brain and a good mind. The study here is entitled "Development of above normal language and intelligence 21 years after left hemispherectomy."  After they removed the part of the brain claimed to be the "center of language," a subject developed "above normal" language and intelligence. 

Then there is the case of Alex who did not start speaking until the left half of his brain was removed. A scientific paper describing the case says that Alex “failed to develop speech throughout early boyhood.” He could apparently say only one word (“mumma”) before his operation to cure epilepsy seizures. But then following a hemispherectomy (also called a hemidecortication) in which half of his brain was removed at age 8.5, “and withdrawal of anticonvulsants when he was more than 9 years old, Alex suddenly began to acquire speech.” We are told, “His most recent scores on tests of receptive and expressive language place him at an age equivalent of 8–10 years,” and that by age 10 he could “converse with copious and appropriate speech, involving some fairly long words.” Astonishingly, the boy who could not speak with a full brain could speak well after half of his brain was removed. The half of the brain removed was the left half – the very half that scientists tell us is the half that has more to do with language than the right half. 

What is also interesting in the new study is that when we cross-compare Figure 1 with Table S3 (in the supplemental information) we find that the patient with the largest brain (after the hemispherectomy operation) had the lowest IQ, and that the patient with the smallest brain had the highest IQ.  In Figure 1 the brain of the subject with an IQ of 80 (subject HS6) looks much larger than the brain of the subject with an IQ of 99 (subject HS4).  Such a result is not suprising under the hypothesis that your brain is not the source of your mind. 

Saturday, November 23, 2019

If Accidents Can't Make Tables, How Can They Make Super-organized Biological Wonders?

Professors tell us that biological complexity has arisen through blind processes of evolution. They teach that random mutations and survival of the fittest have been sufficient to produce all the wonderful innovations we see in biological organisms.

To shed some light on whether this is a tenable notion, let us do some calculations that will help clarify how improbable it is that a very simple accidental invention could occur. If we are to imagine evolution producing some biological innovation, we have to allow that at least some simple invention would have to occur by chance before any biological reward would be achieved. For it is never true that an organism gets survival value by just developing something with one part or two parts. Everything that we can think of that is useful requires at the very least quite a few parts organized with some coordination. For example, before it could yield any biological reward, even the simplest vision system would have to be at least as complex as, say, a table. And before it could yield any biological reward, even the simplest wings would have to be at least as complex as a table. Both of these things (vision systems and wings) must actually be vastly more complicated than a table to work in even the most primitive way.

So let us use a table as an example of a very simple invention. How improbable is it that random pieces of wood in a forest would assemble in such a way as to make a table? If we find that this isn't too improbable, something that we might expect to see after a few thousand tries, it might bolster the idea that blind nature can accidentally make inventions.

We can define a table as a portable flat surface elevated by table legs. The requirements for a simple table are as follows:
  1. there must be a table top
  2. the lower surface of the table top must have four peg holes
  3. there must be four table legs that fit into the peg holes.
The visual below shows the parts that are needed (ignore the ring feature shown in the legs, which aren't necessary for the table working).  We see the underside of the table top, with its four peg holes into which the table legs can fit. 

Conceivably there could accidentally occur in nature some items that might act as the table top and the four table legs. We can imagine several logs accidentally bound together by vines that might end up looking a little like a rectangular table top. If the logs had varying widths, there might be gaps between the logs that could serve rather like peg holes.  The "table legs" could be four other logs.

Given such a short requirements list, at first it may not seem too improbable that a table may form by chance. But let's do some math to get a clearer idea of the chance of such a thing forming accidentally.

To do the math, let us imagine a little machine we may call a Table Part Tumbler. The machine will be a spinning box, rather like the transparent spinning boxes they often use to randomly draw lottery numbers. Let us assume that this Table Part Tumbler is a cubic box that is two meters wide. Let us assume that there is a table top somewhere inside that volume of space. We will also assume that there are four table legs somewhere in this volume of space.

We can imagine that this box will be electrically powered, and spinning for a long time. We can imagine the box equipped with some artificial intelligence detector that will cause it to stop spinning whenever all four table legs fit into the four peg holes. The spinning may cause a table leg to accidentally enter one of the peg holes, or accidentally fall out of one of the peg holes. But once four peg holes are filled, the machine will stop spinning, because a table has been accidentally constructed.

Now these table legs could have any orientation at all in three dimensional space. They could be pointing straight up, or they could be pointing sideways, or they could be pointed at some angle to the left or the right. But for the table legs to accidentally fit into the pegs, the legs must be perpendicular to the underside of the table top, pointing at one of the leg holes. How can we calculate the chance that a leg would be pointing in such a direction?

Here is a method that can be used. Let us assume that a table leg is about an eighteenth of a meter in width (about two inches). Now consider the top surface of our cubic box that is two meters across. In that top surface (two meters wide) there will be about 36 by 36 little areas as wide as one of these table legs. So you can imagine some 1296 little circles on the top face of our box. 

There are also five other faces of the cubic volume to consider: the side faces of the box, and the bottom face of the box. We can also imagine 1296 little circles on each of the four side faces of the box, and 1296 little circles on the bottom face and top face of the cubic volume, as in the diagram below:

To imagine an orientation of a table leg (its position in 3D space), we can imagine a line between one of these circles on the one face of the cubic box, and another circle on some other of the box's six faces. But if a table leg is oriented randomly in 3D space, each of the 1296 circles on the bottom face of the cubic volume can connect to any of 1296 circles on each of the other five faces of the cubic box (which is a total of 6480 circles).

So under these assumptions there will be a total of 1296 times 6480 ways in which a table leg could be oriented in three-dimensional space, or 8398080 possibilities. This is an example of what is called a combinatorial explosion. Such huge expansions of the number of possibilities occur all the time when we consider the number of ways parts can be arranged in three-dimensional space.

Given 4 leg holes in the table, the chance of a particular table leg having the right orientation to fit into one of the leg holes would only be about 1 in 8398080 divided by 4, or about 1 in 2099520. I say “divided by 4” because there are four leg holes that a particular table leg can fit into.

So the chance of a particular table leg fitting into one of the leg holes would be only about 1 in 2099520. But what would the chance be that all four of the legs would accidentally fit into the leg holes at the same instant? Since the probability of each leg fitting into a peg hole is an independent probability, we follow the rule that to calculate the chance of four independent events occurring, we multiply together the probability of each occurring. That gives us a probability of 1 in 2099520 to the fourth power. This is a probability of about 1 in 1.94 X 1025 In this model, the tumbling of the Table Part Tumbler can cause a leg to either fall in a leg hole or fall out of a leg hole. The odds would be greatly reduced if there was some rule that legs always stay in leg holes, but given the tumbling that is occurring, we should not assume such a rule. 

If there were just one of these Table Part Tumbler machines, the chance of a table being produced in a billion years would be very low. Let's imagine that each second of spinning produces a different combination. There are about 3 quadrillion seconds (3 x 1016) in a billion years. But with a probability of only about 1 in 1.94 X 1025 of the table legs all fitting into the peg holes at the same time, the chance of a table being assembled during the billion year period is very low, less than 1 in 100,000,000.

Now you may object that when evolution occurs that there is not just one organism, but many organisms in a population. So perhaps the odds would be better. But they wouldn't be. Each spin of our Table Part Tumbler is like a random mutation in a particular organism, occurring in one particular spot of the organism. Even if there is a very large population of organisms, we should not expect that there will be more than one random mutation per second in one particular part of any of those organisms. For example, even if there are millions of eyeless fish in some particular population, fish that are being born and dying at various times, we would not expect that there would be more than one mutation per second in this entire population corresponding to the little spot of the fish where it might have an eye.

Moreover, for the sake of conceptual simplicity, our model of the Table Part Tumbler has ignored several difficulties that would worsen the odds very much. Consider the following:

(1) The model assumes that there are four peg holes that match the size and shape of the four table legs. But if the model were to better simulate random evolution, then both the width of the table legs and the width of the pegs would be randomly varying, and both the shape of the table legs and the shape of the pegs would be randomly varying, which would very much worsen the odds of the table forming.  
(2) The model has done nothing to factor in the extremely low probability of three or four logs being linked together by vines so you would have a flat table-like surface with four gaps resembling peg holes. 
(3) While wood logs might last for a very long time, after not many years there would occur decay that would rot away any vines that linked together three or four logs to make a flat table top. So if you ever were to have a freak occurrence that created a flat surface resembling a table top with peg holes, by vines linking together logs, such an improbable arrangement would not persist for longer than a few centuries. So instead of having a billion years for the table legs to fit into the table pegs, there would actually be only rare centuries (occasionally occurring during million-year periods) in which there was a possibility of such a fit. 

Altogether these factors would make it quadrillions of times less likely that the table would ever randomly assemble from accidental events in a forest. Given such factors which would vastly worsen the chance of a table being formed accidentally, and the very low probability previously calculated for the chance of all four legs fitting into the peg holes, it seems fair to conclude that the chance of a table (consisting of five or more parts fitting together in the right way) being assembled accidentally on any forest on Earth during a five-billion year period is less than 1 in 100,000,000.  Such an estimate is consistent with the fact that no one has ever observed any table-like structure (consisting of 5 or more parts fitting together in the right way to make a table) that accidentally formed in a forest. 

What does this exercise suggest? It suggests that the chance of even the simplest invention (requiring five or more parts) occurring from random events is very, very low, even given billions of years for random mutations to occur. We can put the matter concisely by saying: typically even the simplest of inventions (requiring exactly the right organization of five or more parts) are extremely unlikely to occur by chance, even if there are quadrillions of random attempts. In the crude mathematical model presented above, there are more than a quadrillion attempts, but the likelihood of the table accidentally appearing is still very, very low. 

These calculations are consistent with the average man's intuitive insight on this matter. The average man intuitively grasps the general truth that useful feats of construction requiring multiple parts fitting together do not occur by accident. 

A table is a ridiculously simple thing compared to biological innovations such as prokaryotic cells, eukaryotic cells, eyes, wings, cells, DNA, and the molecules needed for photosynthesis and respiration. What would the odds be if we were to calculate the chance of the simplest prototype of an eye appearing, or the simplest prototype of a cell, or the simplest prototype of one of the proteins needed for a vision, or any of thousands of similar things? It would be some probability incredibly smaller than the probabilities I have mentioned concerning the accidental appearance of a table. 

These considerations strongly suggest that the origin of complex biological innovations by random mutations and natural selection is impossible. Is there some way that natural selection can get us out of this jam? No, there is not. Natural selection or survival of the fittest can only get started (in regard to some biological innovation) when some biological innovation progresses to the point where some survival advantage is yielded. We may call this point the rewards threshold. Achieving such a reward threshold will always require at least some biological invention vastly more complicated than the very simple invention that is a table. And in almost every case the rewards threshold will not be reached until there is some biological innovation far more complicated and vastly more unlikely to occur by chance than a table.

Inside the human body are more than 20,000 types of protein molecules. Most of these protein molecules are complicated things, usually consisting of a special arrangement of more than 300 amino acids. Protein molecules only are functional if they fold in just the right way to achieve a particular three-dimensional shape. A slight change in the sequence of amino acids in a protein molecule will prevent it from folding, and will make the molecule useless.  A protein molecule cannot originate through some process of accumulation, because the molecule is useless if only a third of it or half of it exists.  Natural selection will not do anything to move a non-beneficial protein molecule closer and closer to a state of being beneficial.  On a biochemical level, we may say that there are more than 20,000 complex inventions in each of our bodies, those inventions being our protein molecules.   How many of these would we expect to exist, under current evolutionary assumptions? Not a single one of them.  The problem of explaining the origin of protein molecules was unknown to Darwin, who knew nothing of the immense complexity of either protein molecules or cells. 

It is easy to roughly calculate the chance of a functional protein molecule appearing by chance.  There are 20 amino acids used by living things, and the number of amino acids in a human protein varies from about 50 to more than 800. The scientific paper here refers to "some 50,000 enzymes (of average length of 380 amino acids)." According to the page here, the median number of amino acids in a human protein is 375, according to a scientific paper. The simplest calculation you could make is to calculate that the chance of a protein molecule appearing in its current form from a chance combination of amino acids is about 1 in 20 to the 375th power.  But that assumes that the protein molecule would not be functional unless it was exactly the way it is.  We do know of many reasons for assuming that for a protein molecule to be functional, a protein molecule has to be nearly the same as it is. Protein molecules are highly sensitive to mutation changes, so sensitive that changing randomly changing ten or twenty amino acids will typically disable the protein. This paper here estimates a probability of about 34% that a random amino acid change will produce a "functional inactivation" of a protein molecule. But that doesn't quite mean that a protein molecule has to be exactly as it is to be functional. 

Let us generously assume that there are many variations of a particular protein molecule that would still be functional.  A reasonable way to allow for such variation is to assume that only half of the amino acids need to have their current arrangement.  That would still leave you with a probability of about 1 in 20 to the 187th power for the chance of a typical protein molecule appearing from a chance combination of amino acids.  That likelihood is about 1 in 10 to the 243rd power, which is smaller than the chance of you guessing correctly all of the ten-digit telephone numbers of 24 consecutive strangers. It's a likelihood so small we would never expect it to happen by chance in the history of the observable universe. 

In his interesting recent book Cosmological Koans, which has some nice flourishes of literary style, the physicist Anthony Aquirre tells us about just how complex biological life is. He states the following on page 338:

"On the physical level, biological creatures are so much more complex in a functional way than current artifacts of our technology that there's almost no comparison. The most elaborate and sophisticated human-designed machines, while quite impressive, are utter child's play compared with the workings of a cell: a cell contains on the order of 100 trillion atoms, and probably billions of quite complex molecules working with amazing precision. The most complex engineered machines -- modern jet aircraft, for example -- have several million parts. Thus, perhaps all the jetliners in the world (without people in them, of course) could compete in functional complexity with a lowly bacterium."

Our Darwinist professors are blissfully ignorant of the math that crushes their explanatory pretensions. Acting rather like Darwin, who had no interest or ability in mathematics, our Darwinist professors pay no attention to combinatorial explosions, and in general pay little attention to mathematics. When they do mathematics, it is usually some type of tangential side calculation rather than the type of calculation that is most relevant to the likelihood of Darwinian evolution. What Darwinist professors mainly do is tell stories, and concentrate on narrative repetition, endlessly repeating claims that miracles of complex construction occurred by accident. But such thinkers are careful to never use the unintentional-sounding word "accident" when describing their theory of a 100% unintentional origin of biology wonders. Instead, they use the very intentional-sounding phrase "natural selection" to describe their theory of a 100% unintentional origin of biology wonders, which isn't terribly forthright. 

The lack of relevant probability calculations by Darwinist professors bothered the eminent physicist Wolfgang Pauli, discoverer of the subatomic Pauli Exclusion Principle on which our existence depends. Pauli stated the following:

"I should like to critically object that this model has not been supported by an affirmative estimate of probabilities so far. Such an estimate of the theoretical time scale of evolution as implied by the model should be compared with the empirical time scale. One would need to show that, according to the assumed model, the probability of de facto existing purposeful features to evolve was sufficiently high on the empirically known time scale. Such an estimate has nowhere been attempted though."

Pauli also stated the following about Darwinist biologists:

“In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational’, they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle’.”

In general, Darwinist professors ignore the mountainous improbability of parts fitting together to make complex innovations. Our Darwinist experts typically speak as if having the parts for something is about as good as  having that thing, ignoring the reality that the more complex something is, the more improbable that parts would accidentally fit together to make that thing, even if all the parts were present.  How often have we heard SETI enthusiasts speaking as if having "the building blocks of life" in space (by which they mean mere amino acids) was almost as good as having a living thing (which requires at least a fantastically improbable special arrangement of such building blocks)? 

Roughly speaking, we can say that the improbability of a complex innovation appearing accidentally usually rises exponentially and geometrically as the number of parts needed for that innovation undergoes a simple linear increase, in most cases when a special arrangement of the parts is required. Similarly, the improbability of you throwing a handful of cards into the air and having them all form into a house of cards will rise exponentially and geometrically as the number of cards in your hand undergoes a simple linear increase.  Getting a two-card house of cards by accident isn't too hard, by having two cards lean together diagonally. But if all the humans in the world spent their whole lives throwing a deck of cards into the air, none of these random throws would ever produce a 20-card house of cards by accident. 

I have spoken about logs, and it is interesting that orthodox biologists are unable to account for the current distribution of animals in the world without resorting to some very unbelievable tall tales in which logs play a part.  For example, there are many similarities between Old World monkeys and New World Monkeys.  Committed to the assumption that such similarities must be because of common descent, Darwinist professors maintain that the New World monkeys are descendants of the Old World monkeys, and that such an ancestry was able to occur because some Old World monkeys rafted across the Atlantic ocean something like 40 million years ago, arriving in the New World.  Such an idea is supremely unbelievable for several reasons: (1) the incredible improbability of a sea-worthy raft appearing accidentally from logs; (2) the almost equally great improbability that any monkeys would ever swim out to sea and jump on such a raft; (3) the almost equally great improbability that such monkeys could ever survive a voyage across the Atlantic.  You can calculate the improbability of item (1) by doing calculations similar to those I have done in regard to a table. The chance of a sea-worthy raft appearing accidentally are almost as bad as the chance of a table appearing accidentally. 

You can make some rough estimates:
(1) Chance per year that a stable raft might accidentally form, one sea-worthy enough to take monkeys across the Atlantic: less than  in a trillion.
(2) Chance that monkeys would ever swim out and jump on such a raft, and stay on it as it floated out to sea: less than 1 in a billion.
(3) Chance that monkeys on such a raft would ever survive a voyage across the Atlantic: less than 1 in a thousand.

The overall likelihood of such a trans-Atlantic monkey voyage per year would be less than the product of all three of these independent probabilities multiplied together: 1 in a trillion times 1 in a billion times 1 in a thousand, which gives a probability of less than 1 in 1,000,000,000,000,000,000,000,000 per year.  The chance that such a thing would have occurred during a 10-million year window of opportunity is, according to such an estimation, less than 1 in 10,000,000,000,000,000.  But as fantastically improbable as such an event would have been, it would still have been trillions of times more probable than the cases of accidental engineering that our biologists ask us to believe in. 

In the willingness of some to accept these supremely absurd tales of trans-Atlantic rafting monkeys, we see what seems to be an example of what is called escalation of commitment. Having wedded themselves to the notion of a purposeless origin of biological organisms, certain people will seemingly accept many an absurdity that follows from such an idea.  At no point does it ever occur to such people to ask whether credulity has been strained too much. Innumerable weighty straw-bundles are heaped upon the camel's back, each a new belief requirement required by the original assumption; and such people will never ask whether the latest one has broken the camel's back, requiring one to finally look for alternatives to the original assumption. Faced with evidence of extremely precise fine-tuning in the universe's fundamental constants, which dramatically subverts their "purposeless nature" assumptions, such people will not hesitate to postulate a multiverse of innumerable universes, which is like piling a million additional straw bundles on the camel's back. 

Tuesday, November 19, 2019

When Professors Make Dubious “All” Generalizations

We can make a classification of different types of generalizations that a scientist might make about nature. 

Type Examples Reliability
“Some” generalizations "Some deaths are caused by cancer."
"Some craters are caused by meteors."
“Some” generalizations can be fairly reliable if supported by an observation showing that in at least one case the generalization holds true.
“Many” generalizations "Many deaths are caused by cancer."
"Many craters are caused by meteors."
“Many” generalizations can be fairly reliable if supported by  observations showing that in multiple cases the generalization holds true.
“Most” generalizations "Most waves are made of water."
"Most birds have wings."
Many “most” generalizations are false, because they are not backed up by any numerical evidence justifying the use of the word “most.” Example: the claim that most mental illness is caused by chemical imbalances. 
“All" generalizations "All things are made of atoms."

Very many or most generalizations using the word “all” are  unreliable. Some of these generalizations may be very large untruths. Typically it is all-but-impossible to prove an “all” generalization. Alarm bells should go off in our minds whenever we hear someone making an "all" generalization. 

Some of the most important “all” generalizations made by scientists have been just plain false.  Scientists once assured us that all heat consists of a fluid called "caloric" flowing from one body to another.  The theory has been disproved. 

Ideally, scientists would follow the practice of not claiming that most things of some type are caused by some particular thing until it was proven that some things of that type are caused by that particular thing; and they would not claim that all things of some type are caused by some particular thing until it was proven that most things of that type are caused by that particular thing. In reality, no such "horse before the cart" rules are followed.  What often happens is that scientists often assert that all things of some type are caused by some particular thing before it has been proven that any thing of that type is caused by that particular thing.  For example, a scientist who is having difficulty selling the idea that some particular mental illness is caused by a chemical imbalance may start teaching that all mental illnesses are caused by a chemical imbalance, even though it has not been proven that any mental illnesses are caused by a chemical imbalance. And the claim that all biological innovations are caused by random mutations was confidently asserted before it was shown that any biological innovation was produced by such a thing. Assertions this presumptive may have argumentative advantages in that they may result in a more forceful rhetorical snowplow. A man asserting "all x's are caused by y" may inspire more confidence than one more humbly asserting "one x was caused by y." 

Scientists have asserted innumerable times that all things are made of atoms. A resounding statement of this dogma was made by the leading physicist Richard Feynman, who stated the following:

If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generations of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or the atomic fact, or whatever you wish to call it) that all things are made of atoms—little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another.”

Here we have a ringing endorsement of the claim that “all things are made of atoms” – a statement by Feynman that makes it sound like such a claim is the Supreme Truth of science. But the frequently made statement that “all things made of atoms” is actually false in several important ways. For one thing, we have thoughts and ideas that are not made of atoms. For another thing, we visually observe some important things that are not made of atoms. A lightning bolt is not made of atoms, but of electrons and photons.  Moreover, we know of various subatomic particles such as protons, neutrons and electrons that are the building blocks of atoms.  These things are not at all made of atoms.  It would seem that the claim that "all things are made of atoms" only made sense when scientists thought that atoms are indivisible particles not made of other things.  

Not made of atoms

Moreover, strictly speaking it is not even correct to say that the sun is made up entirely of atoms or even to say that the sun is mostly made of atoms. An atom is defined as a unit consisting of an atomic nucleus and one or more electrons. Dictionary.com defines an atom in this way: “the smallest component of an element having the chemical properties of the element, consisting of a nucleus containing combinations of neutrons and protons and one or more electrons bound to the nucleus by electrical attraction; the number of protons determines the identity of the element.” But the sun does not contain mainly atoms defined in such a way. The sun consists of a very hot gas containing (1) individual protons, (2) ionized electrons that move around freely without being associated with any proton or atomic nucleus, and (3) helium nuclei consisting of two protons bound together by the strong nuclear force. None of these things is an atom, using the most common definition of an atom.

The sun makes up most of the mass in our solar system. So far from it being  true that “all things are made of atoms,” it is not even true that most of the matter in our solar system consists of atoms. Most of the matter in our solar system is in a hot solar gas that does not consist of atoms (using the most common definition of atoms).

There is an additional reason why the “all things are made of atoms” dogma isn't true. Scientists nowadays tell us that most matter in the universe is not regular matter made of things like protons, electrons, neutrons and atoms, but instead some other very different unknown type of matter called dark matter. But scientists have no understanding of the nature of such dark matter, and have no reason to suspect that it consists of atoms. Since most of the universe's matter is believed to be dark matter radically different from atomic matter, it apparently is not even true that most of the universe's matter consists of atoms.

So the statement that “all things made of atoms” is false in several important ways, even though such a statement has been asserted as a “fact of science” by innumerable scientists in the past 50 years. It would seem that our scientists are prone to make dubious "all" generalizations. So should we then be the least bit surprised if in the future other “all” generalizations claimed to be “facts of science” – such as the claim that all life forms descended from a common ancestor, or that all thoughts come from brains – end up being discarded in the future?

Friday, November 15, 2019

"DNA as Recipe" Is as False as "DNA as Blueprint"

In 1943 physicist Erwin Schrodinger speculated that the chromosomes of a cell “contain, in some kind of code-script, the entire pattern of the individual’s future development and of its functioning in the mature state.” Within a decade, DNA was discovered. But DNA never was found to be anything like some blueprint or recipe or code-script for making a human being. 

The Cambridge English Dictionary defines a blueprint as "a complete plan that explains how to do or develop something." DNA merely contains very low-level chemical information such as lists of the amino acids that make up the proteins in our bodies. Nowhere in DNA is there any of the following:
  1. a specification of the large-scale structure of the human body;
  2. a specification of the structure of any of the appendages of the human body such as legs or arms or heads;
  3. a specification of any organ system of the human body;
  4. a specification of any individual organ of the human body;
  5. a specification of any of the 200 types of cells in the human body;
  6. a specification of any of the organelles that are the building blocks of cells.
There are several different reasons why we know that DNA has no such things. The first reason is that human DNA has been very thoroughly analyzed through multi-year scientific projects involving very large teams of scientists, such as the Human Genome Project and the ENCODE project, and no such specifications have been found in DNA. For example, no one has found any place in DNA where it specifies that humans have two legs or two arms or one neck or two eyes or two ears or ten fingers. The second reason is that only one type of “language” has ever been found used by DNA, the very low-level “poor-man's language” of the genetic code, allowing nothing to be stated other than low-level chemical information such as the amino acids in proteins. Using this “poor-man's language” capable of only stating amino acids or other equally low-level chemical information, it is absolutely impossible to state things such as a complex three-dimensional structure or the anatomy of the eye or the anatomy of the human reproductive system.

DNA only specifies low-level chemical information

The third reason is that if a human DNA molecule were to contain a specification of a human, should a thing would be a fantastically complex instruction that could only be read and interpreted by something in the human womb capable of reading fantastically complex instructions. But nothing like that exists in the human womb. Blueprints are only useful because they are read by human agents smart enough to execute the complex instructions of the blueprints. If a blueprint existed in DNA, it would be something far more complicated than a blueprint for making a home. Such a thing would require some gigantically sophisticated “DNA blueprint reader” capable of reading and executing enormously complicated instructions. But no such thing exists in the human womb. We therefore absolutely cannot explain how a human progresses from a fertilized ovum to a newly delivered baby by imagining that a DNA blueprint or recipe has been read and followed.

Such facts prove in multiple ways that DNA cannot possibly be a blueprint or a program or a recipe for making a human. DNA actually contains less than 10 percent of what is needed to specify a human. A molecule containing all of the information needed to specify a human being would be more than 10 times larger than a human DNA molecule. What we know about the size of the genomes of different organisms is entirely inconsistent with claims that DNA is some kind of blueprint or recipe for making a human. In terms of total number of base pairs, the DNA of humans is more than ten times smaller than the DNA of many amphibians and flowering plants, as you can see in the visual here. We would expect the opposite to be true if DNA contained a blueprint for making a human.

But for decades, mainstream academia has deceived us about DNA, pushing the phony-baloney idea that DNA is some kind of blueprint or recipe or algorithm for making a human. I call this falsehood the Great DNA Myth. The false claim that DNA is a blueprint or recipe for making a human was denounced by Ken Richardson, formerly Senior Lecturer in Human Development at the Open University. In an article in the mainstream Nautilus science site, Richardson stated the following:

"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."

But the Great DNA Myth (that DNA is a blueprint or recipe for making a human) continues to be pushed by many, including the journal Science, the official publication of the American Association for the Advancement of Science. In September, 2019 the publication had a “special issue” entitled “Genotype to Phentotype.” The issue was designed to give us the idea that genotypes specify phenotypes, an idea that is dead wrong. The phenotype (or visually observable characteristics of an organism) is not specified by an organism's genotype (its DNA). DNA merely specifies low-level chemical information, not high-level structural information.

On page 1395 we are told a huge untruth by Zahn, Purnell and Ash, who stated, “The DNA within a human cell, known as the genotype, provides a blueprint to direct a host of processes for building an embodied organism.” Here we have the two biggest fables about DNA, the myth that it is a blueprint, and the myth that the passive chemical information repository that is DNA “directs” things, as if it were almost some intelligent agent. The fallacy of using words such as “directs” about DNA is debunked by biologist Richardson in his Nautilus article, and he also debunks the “DNA as blueprint” myth by stating, “there is no prior plan or blueprint for development.” 

Introducing some of the papers in the “special issue,” Zahn, Purnell and Ash state, “We examine cases in which various cells and traits are specified by DNA mutations or epigenetic changes.” But humans have 200 different types of cells, and DNA does not contain a specification of any one of them. The “special issue” has a paper with the misleading title, “Mapping human-cell phenotypes to genotypes with single-cell genomics.” But the paper does not at all describe how any cell phenotypes or structures are specified in DNA genotypes. It merely mentions some cases in which rare DNA mutations can affect a cell to produce a disease.  The paper has a visual which attempts to illustrate the idea of some mapping between genes and cell types, but it's just a speculative "something like this could exist" type of thing; and instead of listing specific genes, the genes listed in the mapping are listed as "Gene 1", "Gene 2", "Gene 3," "Gene 4," and "Gene 5." Such speculative illustrations do not constitute any case of showing that a cell type is specified by DNA or genes. 

At a biology "expert answers" site, we read an expert answer telling us that "DNA does not have instructions for how to build a cell," and also that DNA does not even specify how to make the mere membrane of a cell. DNA does not specify any type of cell, and does not even fully specify the things that are smaller than cells. Cells are built from smaller units called organelles, and even their structures are not specified by DNA. When we look at the lowest level of chemical structure, and look at proteins, we find that even those are not fully specified by DNA. DNA specifies the amino acid sequence of proteins, but not their three dimensional shapes.  The mystery of how proteins acquire such three-dimensional shapes is the unsolved problem of protein folding, which scientists have not solved despite decades of laborious efforts. Claims that the three-dimensional shapes of proteins are simply consequences of their amino acids sequences (listed in DNA) are disproved by the failure of ab initio methods to reliably predict the shapes of proteins from their amino acid sequences, and also by the dependency of a large fraction of protein molecules on other molecules (so-called chaperone molecules) in order to achieve their three-dimensional shapes.  A scientific paper about such ab initio protein structure prediction (which uses only the amino acid sequence) tells us, "Currently, the accuracy of ab initio modeling is low and the success is generally limited to small proteins." 

The Genotype to Phenotype “special issue” also very strangely includes a paper entitled “Microbiomes as source of emergent host phenotypes.” Talk about grasping at straws. Your microbiome is the set of all microbes living inside you, or the total DNA of all the microbes living inside you. You will not solve the problem that DNA does not contain a blueprint or recipe for making a human by trying to look for instructions for making a human inside the DNA of microbes living inside a human. The DNA of such microbes suffers from exactly the same limitations of human DNA, limitations which prevent it from being anything like a blueprint or a recipe for building large three-dimensional structures.

None of the papers in the Genotype to Phenotype “special issue” provide anything that should prevent us from thinking that Zahn, Purnell and Ash were feeding us baloney when they stated, “The DNA within a human cell, known as the genotype, provides a blueprint to direct a host of processes for building an embodied organism.” There is zero evidence that DNA is a blueprint for making a human, and we know of several reasons why it cannot be any such thing.  Given its physical limitations limiting it to listing low-level chemical ingredients, it is utterly impossible that DNA could do any such thing as directing or specifying even a single process, let alone "a host of processes."  The biochemical processes inside organisms are gigantically complex, far too complex to be specified or directed by the kind of minimalist "bare bones" poor-man's language that is the genetic code used by DNA,  capable of listing only sequences of low-level chemicals.  Below we see a description of one of these gigantically complex processes, from a biochemistry textbook. 

complicated biology process
Immensely complicated biochemistry of vision

On page 26 of the recent book The Developing Genome, Professor David S. Moore states, "The common belief that there are things inside of us that constitute a set of instructions for building bodies and minds -- things that are analogous to 'blueprints' or 'recipes' -- is undoubtedly false." Describing conclusions of biologist Brian Goodwin, the New York Times says, "While genes may help produce the proteins that make the skeleton or the glue, they do not determine the shape and form of an embryo or an organism." Massimo Pigliucci (mainstream author of numerous scientific papers on evolution) has stated  that "old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading." Neuroscientist Romain Brette states, "The genome does not encode much except for amino acids."

In a 2016 scientific paper, three scientists state the following:

"It is now clear that the genome does not directly program the organism; the computer program metaphor has misled us...The genome does not function as a master plan or computer program for controlling the organism; the genome is the organism's servant, not its master."

Debunking the idea of DNA as a program consisting of algorithms, biologist Denis Noble states the following:

"No complete algorithms can be found in the DNA sequences. What we find is better characterised as a mixture of templates and switches. The ‘templates’ are the triplet sequences that specify the amino acid sequences or the RNA sequences."

In the book Mind in Life by Evan Thompson (published by the Belknap Press of Harvard University Press) we read the following on page 180: "The plain truth is that DNA is not a program for building organisms, as several authors have shown in detail (Keller 2000, Lewontin 1993, Moss 2003)."  Scientist Jean Krivine presents here a very elaborate visual presentation with the title, "Epigenetics, Aging and Symmetry or why DNA is not a program." Scientists Walker and Davies state this in a scientific paper:

"DNA is not a blueprint for an organism; no information is actively processed by DNA alone. Rather, DNA is a passive repository for transcription of stored data into RNA, some (but by no means all) of which goes on to be translated into proteins."

Rejecting the "DNA as blueprint" and "DNA as human specification" ideas, biologist Rupert Sheldrake has written 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."

Geneticist Adam Rutherford states that "DNA is not a blueprint." A press account of the thought of geneticist Sir Alec Jeffreys states, "DNA is not a blueprint, he says."  B.N. Queenan (the Executive Director of Research at the NSF-Simons Center for Mathematical & Statistical Analysis of Biology at Harvard University) tells us this:

"DNA is not a blueprint. A blueprint faithfully maps out each part of an envisioned structure. Unlike a battleship or a building, our bodies and minds are not static structures constructed to specification."

"The genome is not a blueprint," says Kevin Mitchell, a geneticist and neuroscientist at Trinity College Dublin, who adds, "It doesn't encode some specific outcome." "DNA cannot be seen as the 'blueprint' for life," says Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland, who says. "It is at best an overlapping and potentially scrambled list of ingredients that is used differently by different cells at different times." Sergio Pistoi (a science writer with a PhD in molecular biology) tells us, "DNA is not a blueprint," and tells us, "We do not inherit specific instructions on how to build a cell or an organ." Michael Levin (director of a large biology research lab) states that "genomes are not a blueprint for anatomy," and after referring to a "deep puzzle" of how biological forms arise, he gives this example: "Scientists really don’t know what determines the intricate shape and structure of the flatworm’s head."

Ian Stevenson M.D. cited quite a few biologists pointing out the genes and DNA cannot determine the form of an organism:

"Genes alone - which provide instructions for the production of amino acids and proteins -- cannot explain how the proteins produced by their instructions come to have the shape they develop and, ultimately, determine the form of the organisms where they are. Biologists who have drawn attention to this important gap in our knowledge of form have not been a grouping of mediocrities (Denton, 1986; Goldschmidt, 1952; B. C. Goodwin, 1985, 1988, 1989, 1994; Gottlieb, 1992; Grasse, 1973; E. S. Russell...Sheldrake, 1981; Tauber and Sarkar, 1992; Thompson, 1917/1942)."

Biologist B.C. Goodwin stated this in 1989: "Since genes make molecules, genetics...does not tell us how the molecules are organized into the dynamic, organized process that is the living organism."

When we ponder the vastly dynamic nature of the human organism, we may more fully understand the absurdity of trying to explain human morphogenesis by pushing a myth of "the DNA blueprint is read." Blueprints are used to create static things such as buildings.  But a human organism is gigantically dynamic, with a vast horde of diverse cellular activities occuring in most of our flesh.  Each cell is as complex as a factory, and to specify a human (with 200 cell types) you would need (among other things) not merely to specify the structure of each of those 200 cell types, but an intricate description of the activity and processes within those cells.  Such a specification would be as complex as one that not only specified the physical layout of 200 factories, but also one that specified the dynamics of the manufacturing processes and material movements inside such 200 factories. We can think of all too many reasons why such vast complexities could never be specified by a molecule merely listing low-level chemical ingredients.  

Some concede that DNA is not a blueprint, but then say that DNA is a recipe. It is just as false and misleading to claim that DNA is a recipe as it is to say that DNA is a blueprint.  Let's start with the definition of "recipe." The Cambridge English Dictionary defines "recipe"  as "a set of instructions telling you how to prepare and cook a particular food, including a list of what foods are needed for this," giving no other definition. DNA does not tell us how to prepare and cook a food, so it is absurd to be calling DNA a recipe. 

A recipe is not a mere list of ingredients, but a set of assembly instructions on how to make some edible food using those ingredients -- instructions such as "mix for 2 minutes on medium speed of mixer," "chop up almonds and pour them into mixing bowl," "pour mixture into a cake cooking pan," and "bake for 35 minutes at 375 degrees." DNA specifies chemical ingredients, but does not specify any steps or algorithm for using such ingredients to assemble complex things such as cells or organs or reproductive systems or organisms. So it is false to say that DNA is a recipe, unless you merely say that DNA is a recipe for making the low-level chemical units called polypeptide chains.  Because it contains no high-level assembly instructions, DNA is neither a recipe nor a program for making a human, any organ system of a human, any organ of a human, any appendage of a human, or any cell type of a human. 

The Great DNA Myth that DNA is a blueprint or recipe or program for building organisms is not some careless error comparable to someone clumsily saying that there are only 7 planets in the solar system. The claim that DNA is a blueprint or recipe for building organisms is a falsehood typically told by certain people who need to tell this particular falsehood to defend unbelievable claims they wish to defend.   I will leave for another post a discussion of the ideological motivations for this misinformation that has been peddled for decades by esteemed authorities in academia.