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Our future, our universe, and other weighty topics


Saturday, February 27, 2016

Genetic Resisters: A Science Fiction Story

John and Mary knew that it would be very difficult for them to have a child in the only way allowed by the government. First they would have to apply to the Office of Genetic Enhancement and try to get a pregnancy permit. As part of their application they would have to supply blood samples. Their genetic characteristics would be analyzed, and if either the father or mother was found to be genetically deficient, the permit would be denied. If the permit was allowed, John and Mary would have to begin the standard government approved procedure for having a baby.

The first step would be for Mary to go to the doctor's office at the right time of month, to supply an ovum. Then while Mary was at home, that ovum would be genetically altered, according to the genetic plan that the government computer had recommended. In the laboratory, the ovum would be artificially fertilized, using sperm supplied by the father, sperm that had also been genetically modified. Then Mary would have to come back to the doctor's office, so that they could implant the fertilized ovum in her womb.

This all seemed like a horrible procedure to Mary, who wanted to have a baby the old- fashioned way. So John and Mary made love without using any contraceptives. After a few weeks, Mary thought she might be pregnant, so she went to the doctor to confirm her pregnancy.

What's your pregnancy permit number?” asked the doctor.

I'm afraid I cheated,” said Mary. “I got pregnant the old-fashioned way.”

Interesting,” said the doctor. “Now let me give you some pills you need to start taking immediately.”

Mary took the pills. A week later Mary was arrested, and transported to the Office of Genetic Enforcement. She was interrogated in a small brightly lit room by a government official named Todd Conklin. 


 So what's your reason for violating the law?” asked Conklin.

I didn't want to go through the standard procedure,” explained Mary. “It's so cold and mechanical. Besides I've heard horrible stories about the genetic freaks.”

Oh, come now, I hope you don't believe that kind of anti-science propaganda,” said Conklin. “Every single genetic intervention approved by the government computer results in wonderful biological improvements.”

Yeah, right, that's the official story,” said Mary skeptically. “But I've heard the truth. Lots of times those so-called 'genetic enhancements' backfire, and the result is somebody like a kid with fins for hands, or a child with a single eye above his nose or a kid with a tongue that hangs way out of his mouth.”

Lies!” shouted Conklin. “Those are just fables told by anti-science government haters. All genetic enhancements result in wonderful benefits for the child. Look, don't you want your country to win the Gene Race?”

I've heard about that Gene Race, but I don't even know what it is,” said Mary.

I'll explain it to you,” said Conklin. “Once genetic enhancements were introduced, it became clear that it was a gigantic race between the different nations, a race that would determine which country would control the world. Whichever country made its citizens stronger and smarter would have a decisive advantage over all other nations. So all the biggest countries started a crash program to enhance their national gene pool. That's the Gene Race.”

I don't care if our country loses that race,” said Mary. “Let some other country win the prize.”

It's not a race for a prize!” thundered Conklin. “It's a race to see who will control the world!”

Well, I don't care about that,” said Mary. “I'm going to go ahead and have my baby the natural way.”

No you are not,” said Conklin. “Your doctor followed the government regulations. As soon as you announced that you had become pregnant without a pregnancy permit, he gave you abortion-inducing pills, as is required by law. They must have worked by now.”

Mary started crying.

Look, I'll let you off this one time,” said Conklin. “But this is going on your record, and don't let it happen again, or you'll be looking at some long jail time.”

Mary thought long and hard about what to do next. Finally she decided on a drastic course of action. She would try to persuade her husband to join her in fleeing to another country, a small, backward country that still allowed natural births. But when Mary told her husband about her plan, he resisted.

Let me check out that country and see whether it's too primitive for us,” said John.

After doing some research John told Mary he thought the country was way too backward to live in.

I've checked out that country, and it's so primitive you wouldn't believe it,” said John. “They don't even have wall-to-wall holographic screens there. Can you believe it?”

But I want to live there, and have a child the natural way,” insisted Mary.

That place is so damn backward,” complained John. “They don't even have house robots. You have to clean your house yourself and cook you own food. Can you imagine living in such a stone-age fashion?”

I don't care about that!” shouted Mary. “I'll cook the food and clean the house myself. I just want to have a baby the natural way, without doing some gene gamble that may give us a kid with green skin or long floppy ears.”

Finally Mary was able to persuade John. They both moved to the small, backward nation, and had a child the old-fashioned way. But John almost divorced Mary after the shock of discovering that he would have to shop for food himself, rather than just telling a robot to go fetch his groceries at the stores.

Tuesday, February 23, 2016

They Keep Feeding Us "Explanation Is Near" Baloney

Judging from orthodox Darwinian theory, we should expect to see fossils appearing in larger and larger sizes, at a steady rate of progression between 2 billion years ago and 100 million years ago. But the fossil record shows no such thing. Instead, we see very little fossil evidence of life prior to the Cambrian era about 540 million years ago. But during the Cambrian era (between about 540 million years ago and 485 million years ago), there is a sudden surge of fossils in the fossil record. This sudden blossoming of life during the Cambrian era is known as the Cambrian explosion. This sudden surge is quite a problem for orthodox biological theory.

The largest categories of life are called phyla. Most of the major phyla first appear in the fossil record during this relatively short Cambrian era. The Cambrian explosion may be described as an information explosion or a body plan explosion. The Earth seems to have suddenly got implementations of all these body plans there was no sign of before. How could that have happened?

An article on February 16th in the journal Nature seems to suggest that a solution to this great puzzle may be near. The article headline says the following:

An evolutionary burst 540 million years ago filled the seas with an astonishing diversity of animals. The trigger behind that revolution is finally coming into focus.

But when we read the article we are disappointed. The only “trigger” described is a rather slight increase in oxygen. That's hardly an explanation for this astonishing information explanation. The article covers up the difficulty by completely failing to even mention that the sudden appearance of such a large variety of highly developed animals in the fossil record is a difficulty for the prevailing account of evolution.

Imagine if you and your spouse go out to a movie. You come back and see on your dining room table there are several freshly typed books describing the US and its cities. You are puzzled: where did this come from? But suppose your spouse suggests this answer: the explanation is that the books are written on paper that she only bought this morning; so the reason they appeared is that only today was there the paper the books needed. That would be a ridiculously inadequate explanation for the appearance of the books. Generally you don't explain the appearance of something merely by mentioning that one of its prerequisites was met at some particular time. Similarly, we cannot explain the sudden appearance of highly developed animal forms by just mentioning that at some particular point one of the prerequisites for such things was met.

The Nature article also seems to have advanced a dubious factual claim, that there wasn't enough oxygen prior to the Cambrian period beginning 540 million years ago. A recent scientific paper authored by ten scientists is entitled, “Sufficient oxygen for animal respiration 1,400 million years ago.” The paper states: “We suggest that there was sufficient atmospheric oxygen for animals long before the evolution of animals themselves, and that rising levels of Neoproterozoic oxygen did not contribute to the relatively late appearance of animal life on Earth. ”

The Nature article is an example of a type of science journalism we see again and again: what I may call the “Explanation is coming” story or the “We're on the brink of explaining this” story. It is as if such articles were written according to the lesson plan shown below.

science journalism


Various versions of these “We're on the brink of explaining this” stories have been appearing for more than 50 years. For more than 45 years I've been reading occasional stories suggesting that scientists are on the brink of solving the mystery of the origin of life. They actually seem to be ages away from solving such a problem. For more than 45 years I've been reading occasional stories suggesting that scientists are on the brink of solving the mystery of consciousness. Our scientists actually seem to be ages away from solving such a problem. If you checked the last 40 years of stories on the protein folding problem, you'd probably read a continual stream of assertions that the solution is right around the corner. But scientists still are stumped by the problem.

You might get the impression from reading these stories that scientists are getting ever-more-triumphant at explaining things. But it may well be that something like the opposite is true. There were many triumphs in explaining things between the year 1850 and the year 1975 (although not all the things that you might list). But in the past 40 years the explanatory triumphs of science seem to have been few and far between. Can you name one big thing that science has explained in the past 40 years, something that was not explained by earlier research? The average person probably can't think of anything. Applied science (pretty much the same as technology) is doing very well, but explanatory science may be sputtering.

It could be that the predominant “bottom-up” approach toward scientific explanation is running out of gas. There is only so far you can go at trying to explain things by trying to describe how little things can add up to big things or by trying to explain a whole just by mentioning the action of its parts. We need to think of more “top-down” explanations in which deep and grand principles cause the things that we are trying to explain. Something like consciousness will not be explained by some little bottom-up explanation involving some nerdy detail of neurons. Our scientists keep looking for some leverage effect by which piddling little things can produce magnificent outputs, failing to suspect that behind the magnificent outputs they are trying to explain may be some equally magnificent cause.

Friday, February 19, 2016

LIGO Doubts Will Persist Unless Replication Occurs

Last week the billion-dollar LIGO project announced the discovery of gravitational waves. It is interesting to examine the very absurd double standard followed by mainstream science when it comes to instantly accepting announcements such as this (based on a single rather questionable observational occurrence) while rejecting evidence for phenomena that is based on decades of experiments.

First, let's look at the LIGO observational event reported last week, and some reasons why it may not be so bulletproof. The scientific paper is here. The observational event occurred on September 14, 2015 at 9:50:45. It lasted only a tenth of a second. Two LIGO observatories recorded an ultra-faint spike at this instant, one in Hanford, Washington, and another in Livingston, Lousiana. The signal was so short-lived and faint that it is best described as a momentary micro-blip.

But there are several reasons for being skeptical about the claim that both observatories observed a pair of distant black holes merging. For one thing, the signal in Louisiana apparently occurred while there was no one in the control room of the observatory. Two scientists had left an hour ago, as reported in this press account. This raises security questions about whether someone could have been messing around in the control room, unobserved.

We actually know that sometimes LIGO would have false signals “injected” into it, by something called the “blind injection group,” but we are assured that this was not such a false signal. But are we sure? The New Yorker reports that the scientists investigated whether one of their colleagues could have faked the signal:

Reitze, Weiss, Gonz├ílez, and a handful of others considered who, if anyone, was familiar enough with both the apparatus and the algorithms to have spoofed the system and covered his or her tracks. There were only four candidates, and none of them had a plausible motive. “We grilled those guys,” Weiss said. “And no, they didn’t do it.” Ultimately, he said, “We accepted that the most economical explanation was that it really is a black-hole pair.”

That is a little less than airtight. Apparently at least four people could have faked the signal, but we are asked to dismiss such a possibility solely on the rather questionable assertion that “none of them had a plausible motive” and the fact that they were questioned.

We should also ask: could other people have faked the signal, other than these four? We would expect such a possibility if the data was stored online, in database servers that could be hacked. Since the reported observation event covered less than a second, it would seem to be an easy job to fake such a thing. If a standard SQL database was used to store the data, someone would merely need to create a short SQL script with a few lines of Update statements. Once you login to a remote server using Telnet or some other utility, you would merely need to login to the database and run the script. Repeat the process on a second server, and you've done everything you need to fake things. Some foreign hacker might have done that from his living room. How can we be confident that such a thing didn't occur? American corporations suffer from all kinds of weird hacking incidents from other countries.

According to this account, an expensive gravitational wave observatory has just been approved in India, because of the observations reported by LIGO. So conceivably foreigners may have had a motive for hacking.


There are other possibilities that don't involve fraud. One possibility is that the incredibly sensitive equipment simply didn't work quite right. That seems all too possible. At this link the equipment is described: “The interferometers consist of suspended mirrors, which reflect the laser beams which are used to sense tiny mirror motions — 1/10,000th the diameter of a proton — caused by the passage of a gravitational wave.” Why should we have much confidence in something so sensitive, measuring something so microscopic that we should doubt the ability of anyone to accurately measure it? These are perhaps the most sensitive measurements that have ever been attempted.

I may also note that the event occurred at the very beginning of a major upgrade. Every software manager knows that new releases or major upgrades are often the source of various types of bugs.


Another possibility is that an earthly signal was detected. The scientific paper claims that such a possibility was considered: “Exhaustive investigations of instrumental and environmental disturbances were performed, giving no evidence to suggest that GW150914 could be an instrumental artifact.” That doesn't sound airtight at all, and the scientific paper gives very few details of how such an investigation occurred. The paper says that they looked for an earthly source that could have produced the signal, and didn't find one. How does that rule out such a possibility? They could have overlooked some earthly source that produced the signal. Since the LIGO observatories are kilometers long, we should expect that they should be sensitive to seismographic events originating from our planet itself.

There are other explanations that could explain the data without gravitational waves being involved. A software error or hardware error could explain the data. There could be a bug somewhere in the very complicated LIGO software that produced a false alarm, due to some programming error.

As for the very brief match of the signals between the two observatories, they are not an exact match, although they look about 95% similar.  Below is the graph from the scientific paper, showing observations from the different observatories during a time of less than a second.  Even though the data from the Hanford observatory has been "shifted" and "inverted" (possibly to make it look like a close match to the data from the Livingston observatory), there is not an exact match between the lines.


 
Such a match could have been found from a “data mining” database query looking for a match. If you give me two random sources of data (such as stock prices in 2006 and bond prices in 2015), collected continuously over months, then with the right SQL query I will probably be able to find some tiny time slice where the data matches up, purely by coincidence, giving a false impression that the same thing was being observed. 

There is another reason for doubt. A scientific paper co-authored by a huge team of scientists estimated that a project such as LIGO should produce 40 detections of gravitational waves each year, from “compact binary coalescence sources.” But so far the LIGO project has announced only one detection, the event of September 14, 2015. Where are all the other such events, that are supposed to be happening almost once a week? This may cast doubt on the LIGO announcement, until such time as other observations are made.

There are two parts of the LIGO announcement. The first is the claim that gravitational waves were detected (which as we have seen is on rather shaky ground). The second is the claim that these waves were caused by a merger of distant black holes. The second claim is speculative, and is not well supported by the evidence.

The scientists had no direct evidence that the claimed signal came from a distant black hole. What they basically did is to do some calculations showing a hypothetical scenario by which a black hole merger might have produced the described signal. But that is not at all the same as showing that such a hypothetical scenario was the actual cause. Given a gravitational wave observation, there are always many possible ways of explaining it astronomically. We are reminded here of the BICEP2 affair, when scientists triumphantly claimed that the signals they detected came from the dawn of time. It was later shown that just such a signal could have been produced by dust. There was no way of even telling from which direction the LIGO signal was coming, so the scientists did nothing to show that the signal came from an exact spot in the sky where black holes are known to exist.

You would think that facts such as these would cause our scientists to be cautious. Science is supposed to require repeated observations, not one-shot wonders. But the scientific community has thrown caution to the wind in this matter. Based on a single rather questionable observational event, the scientific community has acted as if LIGO is proof of gravitational waves and proof of a black hole merger. The first claim is shaky, and the second claim is extremely shaky.

We can contrast this with the situation in regard to evidence for ESP (extrasensory perception). Gathered for over a century, the observational evidence for ESP is currently vastly greater than the one-second LIGO evidence. The Society for Psychical Research and other organizations started publishing experimental data as early as the 19th century. At universities such as Duke University, researchers such as Joseph Rhine spent many years doing experimental research that repeatedly produced spectacular successes, such as the extremely convincing Rhine-Pearce experiments and the equally convincing Pearce-Pratt experiments discussed here, getting results with a chance likelihood of about 1 in 10 trillion. Even more compelling (as described here) was the 73% accuracy rate recorded by a professor at Hunter College, with a person located at another location, making 1850 guesses that should have produced by chance a success rate of only 20%. Also very compelling are ESP tests in recent decades using sensory deprivation studies involving a technique called the ganzfeld technique, and some recent tests with ESP and autistic children, as reported here.

But have our mainstream scientists accepted these results, decades of convincing evidence? No. They keep demanding that more airtight tests be done, no matter how airtight is the evidence. But the same mainstream scientists will instantly accept some “gravitational wave” finding based on a single questionable observational event lasting a tenth of a second. It's a ridiculous case of a double standard. When our mainstream scientists have something that they want to believe in, they seem to have an extremely lenient standard. But when they have something they don't want to believe in, they adopt an exclusionary standard a thousand times more stringent.

It's hard to imagine a more outrageous double standard: if it's something our scientists don't want to believe in, then a hundred years of compelling observations are dismissed as “no evidence”; but if it's something they do want to believe in, then a single questionable observation event lasting a tenth of a second is counted as conclusive proof.

We can imagine if a country club operated in a similar way. It might work like this. If a white person tried to enter the front door of the club, the person guarding the door would simply ask “Are you a member?” and would let in the white person if he answered “Yes.” But if a person of color tried to enter the door, the guard would demand to see a birth certificate, a driver's license, a Social Security card, a work photo ID, and a college diploma. And when all those were produced, the person of color would still not be admitted, on the grounds that there was still doubt about his identity.

Monday, February 15, 2016

The Gigantic Missing Link of Biological Life

The discovery of DNA was one of the great triumphs of science. But ever since this discovery there has been a strange trend which we may call “DNA inflation,” “DNA exaggeration,” or even “DNA apotheosis.” The trend has been to carelessly describe DNA in ever more grandiose terms, regardless of the actual facts. A particularly absurd and careless example of such talk is found on page 31 of the book “Super Genes” by Deepak Chopra and Rudolph E. Tanzi. The authors write the following:

DNA, as the “brain” of the cell, is ultimately in charge of every process...The DNA that's neatly tucked inside each cell is something magnificent, a complex combination of chemicals and proteins that holds the entire past, present, and future of all life on our planet.

This is almost completely inaccurate. DNA is nothing like a brain, and is not even like a computer. DNA is not a “combination of chemicals and proteins,” because it does not contain a single protein. Instead DNA contains chemical information used by the body when it makes proteins. And DNA does not contain “the entire past, present, and future of all life on our planet.”

A statement this outrageous is not very common, but it is very common for writers to inaccurately describe DNA. One very common claim is that DNA is a blueprint that lays out the complete specification of the human body. Another common claim is that DNA is a recipe (or a library of recipes) for making an organism. It is also sometimes claimed that DNA is like a computer program for generating our bodies.

But such statements are not warranted by the facts. Judging from the facts, we must conclude that while DNA uses a code of symbolic representations (the genetic code), DNA is not a blueprint for making a human, is not a recipe for making a human, and is not a program or algorithm for making a human. The facts indicate the DNA is not anything close to a complete specification of an organism, but that DNA is instead something much simpler, mainly just a kind of database used in making particular parts of an organism.

Below are 6 reasons for thinking that DNA is neither a blueprint nor a recipe nor a program for making human beings.

Reason #1: The “language” used by DNA is a minimal feature-poor language lacking any grammar or capability for expressing anything like a blueprint, a recipe, a program or an algorithm for making a human being.

First, let's look at the different ways of specifying a three-dimensional object, and then look at whether any such way could be used by using DNA.

There are two ways in which you can create a specification for building something that will exist as a three-dimensional object. The first way is the blueprint approach, in which you don't specify the steps that must be taken to create the object, but merely specify how the object will look once it is constructed. You can create a kind of blueprint by creating a drawing or image that will specify how the completed object should look. Alternately, you can specify three-dimensional coordinates for each of the parts that will make up the final object. The latter approach is used by video games and in the fancy special effects used in movies. A video game may store a 3D object as a series of 3D coordinates, and then use such coordinates to construct the object virtually.

A different approach for telling how to make a three-dimensional object is what we may call the recipe approach or the algorithm approach. When this approach is used, you merely specify a list of ingredients or parts and a list of steps or operations that will be taken using such ingredients or parts. For example, you might specify steps for making a house without using any blueprint for the house. You could specify a list of building materials and a list of exact operations to be performed on those building materials – a set of instructions. If the set of instructions was sufficiently detailed, they might be sufficient to produce some exact type of house.

But the “language” used by DNA is a minimal type of language that lacks any capability for using either of these approaches. Instead of being a rich language capable of great expression, the language used by DNA is pretty much the poorest, most “bare bones” type of language you can imagine. It's a language unsuitable for purposes other than stating lists of chemicals.

Let's look at exactly how the “language” of DNA works (and I used the word “language” in quotation marks because the expression capability is so limited that it may be an exaggeration to even say that it uses a language). DNA is a molecule containing many nucleotide base pairs, as shown in the diagram below. The base pairs can be either adenine, guanine, cytosine, thymine, or uracil

Combination of these “letters” of the DNA alphabet are used to represent particular amino acids, which are the building blocks of proteins. You have to look at a diagram of the genetic code to understand how particular combinations of these base pairs stand for particular amino acids.

Now this “language” is incredibly constrained. Basically the only thing that you can specify with it are lists of amino acids. To get an idea of how limited this is, imagine if you never learned more than 20 words from your parents or teachers, each the name of some food. Your powers of expression would then be incredibly limited. You might be able to describe some kind of sandwich you wanted by saying something like this:

bread
tomato
lettuce
hamburger
bread

But you absolutely could not specify something like a plan for making a building, a complex machine, or a complex 3D object consisting of many parts existing in different coordinates in three dimensional space.

And so it is for DNA. The “language” used by DNA is effectively 24 words or fewer. Twenty of those words are nouns, each an amino acid. The only verbs are something like the words “start” and “stop,” and possibly also “use” and “ignore.” I include those two words because scientists say that particular genes can be turned on or off.

The table below gives a schematic view of the DNA language. Strictly speaking the only verbs supported are “start” and “stop,” but I have also added “use” and “ignore” to cover the idea of genes that are switched on or switched off. 

You can practice at talking in the DNA language. Here is the algorithm:
  1. State any one of the twenty amino acids in the list above.
  2. Repeat step (1) any number of times.
  3. When you're done, say “Stop.”
Get the picture? Below are some examples of “talking in the DNA language.”

lysine, proline, lysine, valine, serine, tryrosine, stop.
tryosine, valine, proline, lysine, valine, serine, valine, tryrosine, stop

When you try this a few times, you may realize the very small powers of expression of this tiny little DNA mini-language.


Consider the “blueprint” approach of specifying a three dimensional object. A piece of DNA cannot specify that some particular body part should exist at some position in 3D space, because the DNA has absolutely no way of expressing positional coordinates. There is no way to say “behind,” “below,” “above,” or “in front of” using DNA, nor is there any way of specifying how much farther something might be behind, below or above something else. Not only is DNA language incapable of expressing where a nose should be located, the language also cannot even express the idea of a nose. All that DNA can do is to specify some proteins that might be used by the nose. Even that specification is incomplete, because DNA only tells which amino acids are used by a particular protein – it does not specify the shape of a protein (proteins typically have extremely complicated 3D shapes involving lots of folding and twisting).

But what about the “recipe” way of specifying something – can DNA do that by expressing a complex algorithm or list of steps such as we would need to have a program for making the human body? No, it cannot. Expressing an algorithm like that requires a language capability that DNA doesn't have. Consider types of instructions contained in recipes or algorithms:

Repeat this step 13 times
Keep doing this step until condition X is met
Keep doing this step but stop when condition Y is met
Position visible part X so that it is connected to visible part Y

Such ideas cannot be expressed by the “bare bones” language of DNA, which can only express lists of amino acids used to make proteins or nucleic acids.

It seems clear, then, that the language limitations of DNA mean that it cannot be something that expresses a blueprint for a human being or a recipe for making a human being. DNA is not a program for making a human.

Reason #2: Even if the “language” used by DNA had the capability of expressing a blueprint or recipe or program for making a human, there would be nothing that we know of capable of interpreting such instructions.

An important fact to consider is that a list of instructions is not sufficient by itself to cause something to get done. You always need some sophisticated agent smart enough to interpret the instructions and execute them. We know this is true for something like a food recipe. Obviously an apple pie won't get cooked just because you have an apple pie recipe on your table – you need a human smart enough to read those instructions and execute them. But what people sometimes forget is that something similar holds true even for computer code. If I write a computer program in some new language called Lingua, just putting that source code on my computer will never cause the program to run. I would also need to have on my machine a highly sophisticated piece of software called an interpreter, something that is reading each of those instructions, and causing some corresponding action to be taken.

What is the relevance of this to DNA? The relevance is that not only do we know of no capability that DNA's “language” has for specifying anything like a three-dimensional blueprint or an algorithm for making a visible three-dimensional object, but we also know of no capability in the body for interpreting such instructions if they existed. So in order for DNA to work as a program for generating the human body, we would need two things: (1) some capability by which DNA could express complex instructions for making visible three-dimensional objects (which are apparently completely beyond the limitations of DNA's feature-poor, minimalist language); (2) some other capability by some other unknown agent capable of acting as a highly sophisticated interpreter of these complex instructions. Neither of these things is known to exist.

It would seem, therefore, that the idea that DNA acts as a program or algorithm for generating the human body is not just impossible, but doubly impossible.

Reason #3: Despite cataloging the entire human genome, and exhaustively analyzing it, scientists have not discovered any part of DNA where a blueprint of the human body or a recipe for making humans is stored.

The Human Genome Project was a federally funded project that completed in April, 2003, after cataloging the entire human genome (all parts of DNA). It was followed up a federally funded ENCODE project designed to further analyze DNA. The results were gradually released over the next decade. Now with all this exhaustive study and analysis, we would expect that if there existed such a thing as a blueprint for the human body in DNA or a recipe for making the human body in DNA, that it would have been discovered. But no such thing has been discovered. We have discovered in DNA mainly just a list of chemicals used in constructing proteins, not anything like a specification specifying the body plan of humans or how to construct the intricate machinery of the human body.

When we look at the genes that are most commonly cited as something that may constitute something like body plan information, we find meager evidence indeed: the murky case of what are called hox genes. It has been claimed that hox genes “control the body plan of an embryo along the cradial-caudal (head-tail) axis” by means of a tiny area called the homebox. But the evidence for this claim is very weak. Geneticist Jerry Coyne says this about hox genes: “Their overall function in development - let alone in evolution - remains murky.”

I may note that the “homeobox” supposedly having some relevance to the human body plan is only 180 nucleotides long (the equivalent of about 60 words in the DNA language). This is millions of times too small to store anything like a plan for the human body.

The unwarranted claims about Hox genes are summarized by Joseph Hannon Bozorgmehr at the Laboratory of Systems Biology and Bioinformatics at the University of Manchester (author of this scientific paper).  Bozorgmehr writes the following :

Genes code for proteins and RNAs. They don't code for brains, limbs or body plans. Yet many scientists insist that Hox genes, and other transcription factors, are responsible for "laying out the floor plan" of the organism when all they are observed to do is activate genes in already established segments of the developing embryo. We have known this for 20 years. So why are the 39 Hox genes still portrayed as determining the geometry of anatomy when all they do is bind to DNA and RNA polymerase to affect gene expression in ontogeny?

The meager and murky evidence regarding hox genes notwithstanding, our scientists have not found any clear evidence that DNA stores a blueprint for the human body, a recipe for the human body, or any type of program or algorithm like a body plan. If DNA stored such a thing, there would be abundant evidence of it.

In the short video below, Jonathan Wells (a PhD in molecular and cell biology from the University of California at Berkeley) states very clearly that DNA does not map out a body plan. He states “the body plan, as far as we know, is not in the DNA” (0:33), and states that DNA is “not a blueprint, it's more like a parts list” (1:40). 



Reason #4: If DNA stored a human blueprint or human recipe or body plan, humans would have a much larger DNA than simpler organisms; instead, the opposite is often true.

If body plans are stored in DNA, we should expect that the size of an organism's DNA should be proportional to the size and complexity of an organism. For the same reasons that the blueprints of a skyscraper use much more paper than the blueprints for a house, under a “DNA has the body plan” assumption we should think that the human DNA is much bigger than the size of, say, any flowering plant. But astonishingly, the opposite is true. The chart here shows the relative size of the DNA in different organisms. We see that the size of the DNA (in base pairs) in mammals is much smaller than the size of the DNA of many amphibians and flowering plants. We see on this logarithmic chart that the DNA of some amphibians and flowerings plants holds ten times more information than the DNA of humans.

A related comparison is the number of genes in the DNA. According to this link, rice has between 32,000 and 50,000 genes, while humans have only 20,251 genes. That's the opposite of what we would expect if DNA stored body plans.

Reason #5: The DNA size of humans is insufficient to be a blueprint or recipe for the human body with all its complexities.

Astonishingly our biologists have sometimes assumed that DNA is a complete specification for constructing a human body, but I have never once read a biologist consider whether the information size of DNA is sufficient for such a task. The idea that DNA can store a complete specification for a human being will obviously make no sense if our DNA molecules are not big enough to store such a specification, just as it will make no sense to assume that a postcard can store the names of all members of a club if the club has many thousands of members.

It has been estimated that a DNA molecule has an information size of about 700 megabytes. This is not big enough to store a complete blueprint, algorithm, or program for creating a human being. If you use the uncompressed RAW files used in cameras, it will take about 8 megabytes to store a high resolution photo. This means human DNA has an information size needed to store about 100 high-resolution photos uncompressed. This is not big enough to store a complete specification for making the human body. A recently introduced CT scanner requires 320 scans to map a human body, each scan equivalent to such an 8 megabyte photo. But consider also all the microscopic functionality that would need to be specified, and all of the microscopic details. It would seem that it would require many gigabytes to store a complete plan for building a human, not just 700 megabytes.

Reason #6: If DNA stored a recipe or blueprint for making humans, we would probably sometimes see extremely jumbled bodies resulting from mutations, but we don't see such “scrambled humans.”

This is the weakest of my six reasons, so I'll discuss it only briefly. All parts of DNA are subject to mutations in which random changes occur because of things such as copying errors and cosmic rays hitting part of DNA. If DNA stored the human body plan, it seems that we should expect to see weird examples of “scrambled humans,” such as people born with eyes on their cheeks, people with noses on their chins, people born with ears on their foreheads, and so forth. But we don't see such abnormalities. Genetic mutations can produce serious abnormalities, but the human body seems to be implemented with astonishingly fidelity, more so than we would expect if the body plan for humans was stored in DNA subject to mutations.

The Gigantic Missing Link of Life

The reasons discussed above strongly argue that DNA is not a blueprint, recipe or specification for making a human being. Does this mean that there is nothing like a body plan for making a human? Not at all. Such a plan must exist somewhere. But we don't know where it is located. It does not exist in DNA. Widely described as “the secret of life,” DNA must instead be only one secret of life. There must be some other equally great secret that we have not discovered.

This undiscovered secret – the unknown location of the specification for making a human being – is the gigantic missing link of biological life that we have not discovered.

Where might such information be stored? It might possibly be stored somewhere else in the body, or it might be stored outside of the body. It may well be that the answer lies in some field or force or influence or information system entirely unknown to us.

This gigantic missing link of life can most mysteriously be seen at the moment of life's conception. Once a tiny female ovum has been fertilized by a sperm, how does the fertilized ovum know how to turn into a human baby, rather than a million other possible forms? There is absolutely not in DNA any mechanism by which an ovum or an embryo can look up a list of instructions to follow based on its age. An ovum or an embryo doesn't know how old it is, and doesn't know where to look in DNA to look up appropriate instructions; and DNA does not have instructions organized by biological age, which might be looked up by some ovum or embryo that knew its age. DNA has everything written in a language of about 22 words in which 20 of those words are amino acids – not something remotely suitable for stating any instructions other than protein or RNA assembly instructions.

As Jonathan Wells (a PhD in molecular and cell biology) states near the end of this lengthy scientific paper:

The idea that embryo development is controlled by a genetic program is inconsistent with the biological evidence. Embryo development requires far more ontogenetic information than is carried by DNA sequences.

The problem of how a fertilized ovum can progress to a baby is called the problem of morphogenesis. It is an unsolved mystery that modern biology has not given enough attention. The complete answer must involve much more than just DNA, and we have every reason to suspect that it involves something utterly mysterious that we know little or nothing about. Until this mystery is solved, we cannot plausibly claim that we understand either life or evolution.

Postscript:  My point about morphogenesis and evolution is pretty much reiterated in this book "Morphogenesis and Evolution," where Keith Stewart Thomson (president of the Academy of Natural Sciences in Philadelphia) stated the following (at the beginning of Chapter 7):

J. Maynard Smith (1983) has written that "although we have a clear and highly articulated theory of evolution, we have no comparable theory of development." I would turn this statement around somewhat and say that until we have a general theory of development we are unlikely to be able to derive a complete theory of evolution.

Correct, and you could just as easily change that phrase "complete theory of evolution" to "plausible theory of what drives evolution." 

In this .pdf file, a professor of Mathematical Biology makes this statement:

Although genes obviously play a role in development, knowing the genetic make-up of an organism does not allow us to understand the mechanisms of development—we may know that certain genes impart particular properties to certain cells, but how this then leads to tissue-level behaviour cannot be addressed by genetics.

That is basically a fancy way of saying that a fertilized ovum does not become a baby by following a body plan stored in DNA. 

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."

Biologist Rupert Sheldrake says this about this issue:


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.

An evolutionary biologist notes that "the long-held belief that genes are the unique determinants of biological form in development and evolution has been challenged by an extensive number of commentators."  Among these "extensive number of commentators" are the people mentioned above and the authors of this scientific paper, who note that "gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space."

Thursday, February 11, 2016

Scientists Have Detected Gravitational Waves (Yawn) : Why It May Mean Little

It was announced today that scientists have detected gravitational waves, something they have never previously observed. The gravitational waves were detected from the extremely rare event of the merger of two black holes. The detection was made by the very expensive LIGO project. Although some scientists are speaking as if this is some epic breakthrough, it may have relatively little meaning in the grand scheme of things. Buried within the long triumphant announcement in the Washington Post is this statement: “There is no obvious, immediate consequence of this experiment.”


One reason why the detection of gravitational waves may mean relatively little is that apparently no door has been opened to a new cost-effective method of astronomy. Let's look at the facts about how much was put into LIGO and what the output has been so far. More than 600 million dollars has been invested into LIGO, which required a huge architectural infrastructure. After years of effort, the project has produced a single detection of gravitational waves, from a very rare event involving the merger of two black holes. Does this offer some hope of some great new method of cost-effective astronomy? Quite the opposite. A project in which you spend 600 million dollars for a single observation is millions of times less cost effective than alternatives. I can spend $1000 on a Celestron telescope, and use it to make thousands of observations, for a cost of less than one dollar per observation.

Has the detection of gravitational waves changed our understanding of the universe? No, because the existence of gravitational waves was already predicted by Einstein's general theory of relativity, which almost everyone already believed in. Has the detection of gravitational waves been a case of giving some needed support to a tottering theory that people were starting to question? No, there was already tons of evidence in favor of the theory of general relativity. A new observational confirmation for the theory of general relativity is kind of like giving another billion dollars to Bill Gates.

The interesting questions in physics and cosmology are questions like these:

Why did the universe suddenly begin billions of years ago in the Big Bang?
Why are the fundamental constants of the universe so exquisitely fine-tuned?
Are there any reasons for believing in a universe beyond our own?
Are there any reasons for believing in parallel universes?
Why does light sometimes act like a particle and sometimes like a wave, depending on how we observe it?
What is this strange thing called quantum entanglement, and does it point to a far greater amount of connectivity in the universe than we previously imagined?
Does quantum mechanics imply a new outlook on consciousness, in which the observer is king?
Why is the universe so astonishingly ordered on a large scale?
Why is the vacuum of space relatively empty, when quantum mechanics predicts it should be something totally different, teeming with something like “zero-point” energy?
Why does the universe have its particular set of laws that favor the existence of living things?

As far as I can see, the detection of gravitational waves casts no new light on these questions.

Is there any chance that we might be able to do observations like that of LIGO many times more cost-effectively? Not really. LIGO used a pair of observatories that each used “ultra high vacuum systems” with an L-shape measuring 4 kilometers (2.5 miles) on each side. There is little prospect of being able to shrink something like that to something that your local college can use.

The press stories are comparing the LIGO project to a moonshot. It's nice that this particular moonshot has succeeded, and I congratulate the scientists who achieved this very expensive triumph. But it must be remembered that from a “science payoff” perspective the moon landing program was something of a dead-end boondoggle. After paying a king's ransom for moon rocks, we didn't learn much of anything new. A similar situation may exist in regard to observing gravitational waves. Just as going to the moon to pick up rocks is the opposite of a cost-effective method for geological observations, projects such as LIGO may be the opposite of a cost-effective method for astronomical observations.

Postscript: I may note that gravitational waves have no practical use.  It's a trillion times easier to use electromagnetic waves for communication, and electromagnetic waves are just as fast; so it's hard to imagine that anyone will ever be using gravitational waves for communication. 

Of course, a science mission with no practical benefits may be justifiable if it yields lots of nice visuals, lots of eye candy for the public to enjoy. The mission to Pluto had no practical benefit, but produced some nice visuals. But we have got not a single decent visual from the LIGO project. We could have got better visuals with a $1000 Celestron telescope.  

Post-postscript: It turns out the total LIGO cost was more than a billion dollars. John Horgan asks in Scientfic American whether it was worth the money, and quotes a historian of technology who seems to think the funds would have been better spent in other ways.

Sunday, February 7, 2016

The Man Who Owned America: A Science Fiction Story

In order to understand how Cory Gates became the owner of the United States of America, you have to first go back to those wild days of the 2030's, when the big corporations were starting to fight each other with increasing violence. Each of the big corporations started to hire its own mercenaries, although at first they were just called security contractors or security guards. There were many truck hijackings, computer hacking attacks, and cases of arson; and before long it became apparent that it wasn't just loner crooks doing this. It was the private armies of the big corporations fighting each other.

People were willing to put up with this for quite a while. But when the big corporations started to arm their mercenaries with machine guns and missile-armed attack helicopters, things started to get out of hand. People got tired of being woken up at night by attack helicopters and exploding buildings. People also got tired of stepping over dead bodies in front of office buildings and stores.

So finally someone proposed a radical solution designed to stop the corporate fighting entirely. The idea was to combine all of the country's corporations into one big corporation that would be called America, Inc. That way there couldn't be any violent fighting between corporations, because there would be only one corporation in the country.

The idea caught on, and before long Congress passed the legislation authorizing the big change. All of the corporations were merged into a single corporation called America, Inc. It was a corporation that owned pretty much everything in the country. Almost everyone other than the poorest people owned at least some shares in the new corporation.

But by this time the richest people in the US had become very, very rich. There was, in fact, a single individual by the name of Cory Gates who owned 45% of the stock in America, Inc. After a few years he was able to increase that up to 51%. Once he gained majority ownership, he was able to manipulate things so that his share would get even bigger.

It was all a fancy scheme too complicated to be described here. The scheme involved inverse options, sub-millisecond computerized stock trading, computerized virtual proxies, collateralized debt obligations, and “trapdoor” regulations secretly introduced into the bylaws of America, Inc. You can kind of describe it by saying it was a shrinkage scheme designed to make the share of all minority stockholders gradually dwindle away to be nothing. When the scheme started to take effect, people started to scream bloody murder, saying that Cory Gates was trying to up his ownership of America, Inc. all the way up to 100%. But the scheme was so complicated that no one could really figure it out well enough to stop the scheme from working.

Finally the complicated scheme ran its course. One day it was at last announced that Cory Gates now owned 100% of the shares of America, Inc. It was now finally official. Cory Gates was now basically the owner of the entire country. 



For 30 years Cory enjoyed the perks of being America's owner. The Pledge of Allegiance recited by children was changed to have the following wording:

We pledge allegiance to America, Inc., and to its owner Cory Gates – one corporation under Cory, indivisible, with obedience and subservience expected from all.

Cory lived in the opulence you might expect from someone who owned an entire nation. His bedroom was ten times bigger than a football stadium, and contained 200 different beds, some as large as trucks. Cory liked sleeping in a different bed every night. He would also travel around the country, staying in any home he would pick. Few people could object, because most people's homes had a mortgage with America, Inc being the lender, meaning Cory pretty much owned most people's homes.

People with regular jobs all worked for America, Inc, meaning Cory was their boss. People who refused to work for America, Inc. usually ended up in what they called “unemployment camps,” although the prisoners in such camps were often worked mercilessly. Each prisoner would be controlled by an electronic pain necklace that he could not remove. If a guard saw the prisoners acting up, he would just activate their pain necklaces, causing punishing anguish.

Officially there was still a President of the US during this period, although he was just a figurehead because Cory controlled the whole country. But after decades of being America's owner, Cory finally died of a heart attack.

Cory's will specified that all of his assets should be inherited by his son Todd. Everyone thought that Todd Gates would rule as America's owner, just as his father had. But Todd had no interest in lording over people or living like a king. Todd was only interested in one thing: reading and writing comic books.

So shortly after his father's death, Todd gave a televised speech that announced a radical change.

I have decided to donate all of my shares of America Inc. to the American population,” announced Todd. “Each American will own one share of the corporation. The bylaws of the corporation will be adjusted so that it is strictly forbidden for anyone to own more than one share of the corporation.”

There will no longer be a single person ruling as America's owner,” explained Todd. “The country will be controlled by a President who will be elected by an annual meeting of the stockholders. Since each American will be a stockholder, each American will have one and only one vote that helps decides who controls the country.”

A man listening to the speech in his home was delighted.

Why this almost sounds like that old-fashioned system they use to follow long, long ago,” said the man to his wife. “I've forgotten what they used to call it.”

I think they called it...democracy,” said his wife.