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Our future, our universe, and other weighty topics

Sunday, July 26, 2015

We Do Not Know That Evolution Occurs Mainly Because of Natural Selection

The history of science contains many cases of theories that were oversold by eager apostles. One of the main cases today involves the overselling of the theory of natural selection. In this case many of our biologists are representing as “settled science” the idea that natural selection is the main cause for evolution. The evidence for evolution is good, but the evidence is quite weak that natural selection is the main cause of evolution in large organisms.

Let me clarify the difference between evolution and natural selection. Evolution is the idea that over very long periods of time, species very gradually undergo changes, developing novel adaptions to their environment, with such adaptions sometimes becoming sufficient for one species to evolve into a different species. Natural selection is a hypothesis about the cause of evolution. Natural selection says that evolution occurs mainly because organisms that are more fit to survive tend to reproduce more. Darwin introduced both the basic idea of evolution and the theory of natural selection at the same time, in a book entitled On the Origin of Species by Means of Natural Selection. But it is quite possible to believe in evolution without believing that natural selection is its main cause.

The modern theory of natural selection is all centered around the idea of random mutations. The idea is that the blueprint of a species (found in its DNA) undergoes random changes called mutations, which might be produced by something like a cosmic ray hitting the DNA stored in a cell, or a random “copying error” when the DNA is not copied exactly right. In some cases, it is claimed, these random changes result in a change that is actually beneficial. When such a thing happens, it is claimed, natural selection causes the organisms that had such mutations to reproduce more often than some other organisms in that species which did not have such a mutation. It is claimed that this causes the mutation to be inherited more and more often in later organisms belonging to that species. Such a process, it is claimed, it so powerful that it can account for all kinds of astonishing adaptions in organisms. 
Now the question is: what evidence is there for this theory that natural selection is the main force behind evolution? Although there is lots of historical evidence for evolution (found in the fossil record), there is no significant historical or fossil evidence that natural selection has been the main cause of evolution in large organisms. Think for a moment of the difficulties of ever getting such evidence. In almost all cases when we have a fossil record of some organism that existed eons ago, we don't have DNA from that organism. Even if we had that DNA (from a few dead organisms), it would still not be enough to figure out the history of DNA changes in a species from long ago, and whether or not  natural selection was the cause of evolution in a particular species.

It turns out that getting evidence for natural selection requires an incredibly hard procedure. This procedure has been attempted on some small organisms with very short lifespans (such as bacteria and fruit flies). The procedure might go something like this:
  1. You start out with a population of organisms of some type, and you carefully record the DNA of all of those organisms.
  2. You track the evolution of these organism over many generations, while applying some factor that causes lots of mutations. The DNA of these organisms must be checked at very many times.
  3. You attempt to determine whether useful new adaptions are being evolved, and attempt to determine whether such adaptions (this new functionality of evolutionary novelty) are being produced by natural selection and random mutations.
The experiments that have been done along these lines have produced very modest results. The study here studied 600 generations of fruit flies, finding no change more dramatic than a 20% shorter life cycle. 

Another experiment is Richard Lenski's long-term experiment on bacteria, which has tracked more than 60,000 generations of bacteria. The results of this experiment have been modest, with the main result merely being that the bacteria seem to have developed an ability to digest citrate that it did not have before. Documenting such an adaption is “peanuts” compared to demonstrating that a significant and complicated structural innovation (such as the human eyeball or a wing) did occur because of natural selection (something that no one has ever demonstrated).

Even Lenski's meager result is subject to doubt, as a large fraction of scientific experiments are not replicated when another experimenter tries to replicate them (and in the case of Lenski's experiments, it will be decades before we can determine whether someone is able to replicate his results).

There is a simple reason why experiments of such a type can never show that natural selection is the main cause of evolution in large organisms. The shorter the life cycle of an organism, the more likely it might be for it to evolve beneficial changes because of natural selection. Bacteria such as those in Lenski's experiment have a lifespan about 130,000 times shorter than a human lifespan, and can double their population in only about an hour. It is all too possible that natural selection is sufficient to cause useful adaptions in very short-lived organisms such as bacteria, but is not sufficient to cause useful adaptions in large, long-lived organisms such as animals as large as a dog or larger.

But isn't there some way, in theory, that you could prove natural selection by using large long-lived animals such as mammals? Yes, in theory there is. But it has never been done, and would be a nightmare to do, as it would take ages.

Imagine how the project might be executed. After building some special testing environment (perhaps some special large building), you would start out with a population of some large species with a lifespan of more than decade. You would take samples of the DNA of each organism in such a population. You would then monitor such a population over many generations, frequently taking DNA samples to see how the DNA was changing. Since a generation for such organisms would take at least a year, the project would have to probably last for thousands of years. All in all, it would be a project more difficult than landing men on Mars. No one has ever done such a project, or even one tenth of such a project.

It would seem that for reasons such as these, the theory that natural selection is the main explanation for the evolution of large animals is one that simply is not very susceptible to experimental verification. But what about some other approach? What about some approach in which we get the predictions of the natural selection theory, and then try to verify that such predictions are coming true?

But that doesn't work either. The reason is that the modern theory of natural selection is all centered upon the idea of blind chance. The theory assures us that natural selection will do random stuff we can't predict. So there is not much of a way to match up reality with the predictions of natural selection. For example, natural selection does not give us any predictions about what a particular organism will evolve to in the future. So there is no way to exactly match up predictions and reality when trying to get proof for natural selection.

So from the standpoint of being verified, the theory that natural selection is the main driver of evolution in large animals is on incomparably weaker ground than other scientific theories which do make a host of exact numerical predictions that are repeatedly verified to the letter. Using a theory such as the theory of gravitation, one can make very precise predictions such as the prediction that a particular object released from a particular height will hit the ground 14.5 seconds after it has been dropped. Such predictions have been verified countless times. But the theory of natural selection has no such record of predictive success. Some of the things that are sometimes claimed as “successful predictions” of the theory (such as the discovery of something like DNA) are not actually predictions uniquely predicted by the theory. A nonbeliever in natural selection would have been just as likely to have predicted that something like DNA existed before it was discovered.

Eager to try to prove that natural selection is an important determinant of human traits (or the main determinant), some scientists have resorted to statistical analysis of DNA (the genome). But such studies may not be mathematically sound. In 2009 Phys.org published this article stating the following:

Scientists at Penn State and the National Institute of Genetics in Japan have demonstrated that several statistical methods commonly used by biologists to detect natural selection at the molecular level tend to produce incorrect results. "Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions," said Masatoshi Nei, Penn State Evan Pugh Professor of Biology and the team's leader.

Likewise the paper here states, “Many of the statistical methods for detecting natural selection are unreliable.”

The study Genome-Wide Scans for Footprints of Natural Selection notes, “a puzzlement arises when we inspect how modest is the replication for discovery of different genomic regions between algorithmic approaches or between different studies.”

Given these items, one must wonder whether scientists scanning the genome, eagerly looking for faint traces of natural selection, are much different from UFO enthusiasts scanning photos of Mars and occasionally claiming to have found something important. Given a mountain of data, sufficient time and a huge toolkit of statistical methods to choose from, it is not too unlikely that you may be able to find “faint traces” of exactly whatever it is that you were hoping to find. I may also note that finding some statistical trace of natural selection would not by itself prove that natural selection is the main thing driving evolution in larger organisms such as man. It is entirely possible that natural selection is a relatively minor effect in species with long lifetimes, and the main thing propelling evolution is something else. 

There are also very substantial reasons for doubting that natural selection is the main thing that caused evolution in humans. The best reason I know of is the inability of natural selection to explain dozens of human mental faculties and traits that do not seem to be adaptions that contribute to reproductive success. Consider this question: what is it intellectually that makes a human different from a monkey? There are many things: we have good language ability; we're good at math; we have morality; we are spiritual; we have esthetic abilities that allow us to create and appreciate art; we have inner lives and introspection; we can form abstract ideas and ponder philosophical questions; and so forth. But none of these things are biological adaptions that improve an organism's likelihood of surviving until reproduction. So none of these things can be explained by natural selection. It would seem, in fact, that natural selection theory predicts that such things as these should not even exist. 

 Human traits hard to explain by assuming natural selection

So far from just being a case of natural selection not making predictions that we can verify, the problem seems to be that natural selection theory would seem to make counterfactual predictions about human nature – that you should not have any important characteristics unless they make you more likely to survive until reproduction (in other words, that you should not have most of the things that make you different from a monkey).

The difficulty of using natural selection to explain the origin of man's mental capabilities is compounded by the fact that about 200,000 years ago the population of humanity was believed to be small, as few as 10,000. The fewer organisms there are in a population, the more unlikely that there will be enough mutations for natural selection to produce something useful.

I may point out here that you could not counter these arguments merely by pointing out some evidence that natural selection occurs. Let's consider three different ideas that can be listed in a table.

Hypothesis 1 Natural selection occurs.
Hypothesis 2 Natural selection occurs, and is the main cause of new adaptions or features in small organisms with short lifespans (bacteria, fruit flies, etc.)
Hypothesis 3 Natural selection occurs, and is the main cause of new adaptions or features in large organisms such as humans.

You do not prove Hypothesis 3 by merely proving Hypothesis 1 or Hypothesis 2. Since the reproduction rate of tiny organisms may be thousands or tens of thousands of times greater than the reproduction rate of large organisms, you don't prove Hypothesis 3 by proving Hypothesis 2. So you can't successfully rebut this post by merely citing something that supports Hypothesis 1 or Hypothesis 2.

Given all these problems with the idea of assuming that natural selection is the main cause of evolution in large organisms, why is such an idea being sold as “settled science”? Why are we being dogmatically assured by so many biologists that they understand what caused the appearance of man's higher traits? I think it's a case of premature triumphalism. After first figuring out that evolution is occurring, our biologists should have merely said to themselves: we have completed one lap, but there are still 10,000 laps to go before we understand this. But instead scientists crowned their heads with laurel leaves (and put gold medals around their necks) after completing the first lap – by assuming that the first major book on evolution had also figured out what the cause of it is. It is all too plausible that the actual cause of evolution is some principle or principles far more complex and vastly more deep than the simple idea of natural selection. If we ever understand such a principle or principles, I suspect we will find that it is also the explanation of the origin of life, something entirely unexplained by the theory of natural selection.

It is entirely possible that the main thing driving evolution is some natural mechanism far deeper and more sophisticated than natural selection – some mechanism involving undiscovered laws of nature or undiscovered information processes (or both) that tend to work in a teleological or anti-chaotic manner, causing more and more complex things to emerge from simpler things. Nature could have embedded within it some kind of programming (or something that acts like programming), some wellspring of emergence that acts as an antithesis to the Second Law of Thermodynamics, causing ever-increasing order as time passes. Such a principle might be behind the evolution of man's faculties, the origin of life, and the physical ordering of the universe since the time of the Big Bang.

Wednesday, July 22, 2015

Primordial Puff Piece

This week I saw an outrageous example of puffery in a press release announcing a scientific study. The press release was put out by the Georgia Institute of Technology, and was picked up word-for-word by the popular Science Daily site and other sites. The press release was entitled “Finding the Origins of Life in a Drying Puddle.”

Despite the dramatic title suggesting a solution to the age-old problem of the origin of life, when we read the details of the study we find some utterly boring results that aren't even a major step towards such a goal. Some scientists used a procedure involving wetting and drying cycles, and succeeded in combining amino acids into polypeptides that consisted of as many as 14 units.

To illustrate how minor this result is, I need merely show a diagram of a polypeptide. A polypeptide is like a necklace, and amino acids are like beads on the necklace.

This result (similar to previous results) is about as exciting as stringing 14 necklace beads onto the string of a necklace, or combining 13 individual playing cards into a bridge hand of 13 playing cards. The study does essentially nothing to answer the main problems in the origin of life, which include the staggering problems of the origin of self-replicating molecules, the origin of the genetic code, and the origin of proteins consisting of thousands of amino acids, not just 14.

So what we have here is quite a case of exaggeration by biologists. A press release that should have been humbly titled “Looking for the Origins of Life in a Drying Puddle” has instead been titled “Finding the Origins of Life in a Drying Puddle,” as if scientists have already solved a problem that could easily take them another thousand years to solve.

All in all, this press release tends to raise again the question of whether many of our scientists (who often speak as if they were lords of knowledge) may be closer to being “lords of exaggeration.” The truth is that scientists have made relatively little progress in the past 70 years searching for clues to the origin of earthly life. The task of explaining the origin of life using existing paradigms seems all-but-insurmountable. The concepts of natural selection and evolution really offer no help, because neither evolution nor natural selection can get started until life itself begins.

As I was typing this post, I was coincidentally watching a TV program in which some astronomers talked about the likelihood of life on other planets. One spoke as if the origin of life was as simple as having the right ingredients. Using similar reasoning, we might vacuously argue that we can explain the origin of a computer program by just mentioning that the electrons that make up that program (when it is stored in a computer) were lying around ready to be used.

The problem of the origin of life is a problem of accounting for an “information explosion” that seems inexplicable as a chance event. To get insight on such a thing, we may need a new paradigm that assumes that the information needed for the origin of life was already lurking within the universe, in some mysterious information infrastructure beyond our ken, some cosmic framework involving not just laws of nature but programming. You can't dismiss such a possibility by saying, “That's not allowed, because it sounds like some gift of a deity interested in our existence.” Exactly the same criticism could be made of the theory of gravitation or the theory of electromagnetism, which are equally necessary for our existence.

Saturday, July 18, 2015

The Fallacies of the “Science and Religion Apartheid” Reasoners

When people wish to exclude others from considering any possibility that might be associated with the paranormal or the religious, such people often use a type of reasoning I might call the “that's religion, not science” argument. Most commonly this is used as a rationale for completely excluding any thought that our universe may be the result of something more than just blind chance. If someone, for example, suggests that the origin of the universe may have been some kind of divine creation, such a hypothesis may be excluded under the grounds that such thinking is not science, but religion.

The same reasoning can be used to try to justify a kind of “gag rule” in scientific publications – a rule forbidding mention of anything that might be considered from the world of the paranormal or the religious. Got some evidence that suggests the possibility of some design or purposeful direction in the origin of life or the evolution of life? Sorry, discussing that is not allowed because that's religion, not science. Got some evidence based on near-death experiences that there might be such a thing as a soul that survives death? Sorry, you can't discuss that in a scientific publication, because that's religion not science. Got some evidence that there may be some power of the mind beyond that which neurology can account for? Sorry, you can't present that evidence because that's religion not science. You get the idea. This “that's religion not science” argument ends up being very convenient for the materialist or physicalist, and it has a superficial plausibility.

This type of reasoning involves a kind of “science and religion apartheid” thinking. The idea is that there's the science box and the religion box (like two cardboard boxes on different parts of the floor), and that we have to place a particular idea or writing in either one box or the other. Paraphrasing the famous statement about East and West, you might express this assumption by stating this slogan: science is science, and religion is religion, and never the twain shall meet.

But is this type of reasoning valid? No, it isn't, as I can show with an important historical example. In the 1920's a Belgian priest by the name of Georges LemaĆ®tre first proposed the idea that the universe suddenly began ages ago in a state of inconceivable density that he called a primordial atom. At the time the idea that the universe had a sudden origin was an idea from the world of religion, not the world of science. For one thing, there was no known evidence for such a theory. Scientists favored a different idea, that the universe had existed forever. No doubt many scorned LemaĆ®tre's idea, saying “That's religion, not science.” But in the next few decades the evidence for such a sudden beginning of the universe began piling up. Now scientists accept such an idea, which they call the Big Bang theory.

So we have here an important example of an idea from the world of religion – the idea of the sudden origin of the universe – that started out as unsubstantiated (not science), but then actually became science (and not just trivial science, but one of the most important findings of modern science). What lesson must be draw from this example? The lesson is: an idea should not at all be excluded from further consideration by scientists merely on a basis such as “that's religion, not science.” This example proves that an idea that originally seems more religious than scientific may end up becoming an important part of science.

So the “that's religion, not science” type of reasoning is not valid as some basis for exclusion. But why exactly is this reasoning fallacious? I can give two reasons.

Reason #1: There Are Several Definitions of Science

The “that's religion, not science” type of reasoning takes advantage of the fact that science is defined in two different ways that are quite different. The first definition is what we may call the “facts on the shelf” definition. People sometimes speak of science as the body of facts collected by scientists. Using this definition, you can attempt to categorize almost all theoretical ideas that scientists discuss as being “not science,” on the grounds that they are not yet proven facts. Just as you can exclude almost everything from the world of the paranormal or the religious as “not science,” you can exclude many scientific hot topics such as string theory, the cosmic inflation theory, the multiverse, neo-Darwinism, and many other theories which are not yet regarded as well-proven as, say, the existence of gravitation or the existence of bacteria.

But there's a second definition of science – what we can call the “process” definition. According to this definition, science is the process of seeking truth through systematic efforts that involve observations, experiments, and theorizing. According to this definition, almost anything that involves honest, systematic and well-organized observations, experiments, or evidence-based theorizing is science (whether it be professional science or what is called citizen science carried out by non-professionals). So according to this definition, almost everything that is typically excluded on the basis of being “religion not science” is actually science. That doesn't mean that it's proven to be entirely correct, but merely that it does fall under the category of “the process of seeking truth through systematic efforts that involve observations, experiments, and theorizing,” which is one of the main definitions of science.

So, in fact, it is not all clear that those items typically excluded as being “religion, not science” are in reality “not science.” They may well be science (either today or in the future) depending on which definition of science you use.

Reason #2: Ignoring the Possibility of an Overlap

The second major fallacy in “that's religion, not science” type of reasoning is the assumption that the realm of science truth claims and the realm of religious truth claims are mutually exclusive areas that can never overlap to any degree (so that once we have identified something as a religious truth claim it can be excluded as a science truth claim). The assumption may be illustrated by Model 1 in the diagram below.

Such an assumption may be incorrect, because there may be some overlap between the realm of religious truth claims and the realm of science truth claims. The truthful situation may be as illustrated as Model 2 in the diagram above, in which some truth claims can exist in both the realm of science and the realm of religion.

What reasons are there for thinking that the correct model is the second of these models, not the first? For one, there's the simple fact that human realms of thought do not naturally tend to be entirely mutually exclusive without any overlap. For example, there is a political realm of thought that includes the notion that “all men are created equal.” But the fact that a truth claim of human equality has been made in the realm of politics does not mean that we should exclude it from the realm of science. For example, if you were doing a scientific study on intellectual abilities in different races, it would hardly make sense to say, “I must at the beginning rule out the idea that all races are equal, because the idea that all men are equal belongs to politics, not science.”

Another reason for thinking that the second diagram is the correct one is that we have the huge historical example of the claim “the universe suddenly originated.” That is a currently a claim existing in both the realm of science and the realm of religion. So this proves there is some overlap between the realm of science truth claims and the realm of religious truth claims. We could easily add another “overlap” example involving claims that the universe is exquisitely fine-tuned. I could make a list of statements along these lines by scientists and religious people, without identifying the person who made the statement; and you would have a hard time distinguishing between the statements by the religious and the statements by the scientists.  One might also add as examples of overlap between science and religion some of the items that Fritjof Capra called attention to in his famous book The Tao of Physics: An Exploration of the Parallels Between Modern Physics and Eastern Mysticism.

What is the proper attitude that a scientist should take to a truth claim that he has identified as one that is being made by some religion or religious person? The proper attitude is not one of automatic exclusion because of such a thing, but instead an attitude of indifference toward such a thing. For example, if you are a scientist considering whether there is some evidence for the soul, you should not be saying, “I will rule that out because some religious people believe it,” but instead you should be saying, “I will pay no attention to how many people believe it, but judge the matter purely on the facts and the evidence.”

But such a principle is ignored by many who try to keep science as illogically exclusionary as a 1950's Alabama country club.

Tuesday, July 14, 2015

Was the Cambrian Explosion Caused by Extraterrestrials?

In his book Darwin's Doubt, Stephen C. Meyer calls our attention to an unexplained anomaly in paleontology. When we examine the fossil record, we don't see fossils appearing in larger and larger sizes, at an even rate of progression between 3 billion years ago and 100 million years ago. Instead, we see relatively little fossil evidence of life prior to the Cambrian era about 500 million years ago. But during the Cambrian era 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. The Cambrian explosion is illustrated in the diagram below, from a paper suggesting a prosaic explanation for it. The "known fossil range" lines go back no further than the Cambrian era.

Meyer (who has a PhD from the University of Cambridge) argues that this Cambrian explosion is the result of intelligent design at work in the evolution of life. But there is an alternative to assuming a supernatural hand at work in such a thing. Maybe the Cambrian explosion was caused by extraterrestrials.

We can imagine a hypothetical conversation that could have occurred millions of years ago, aboard an alien spaceship that entered into orbit around our planet.

Xynus: So give me the facts. What is the status of life on this planet?
Zeesin: Our underwater robot probes have confirmed that this planet is an evolutionary dud. There's hardly anything here in the way of life. What a waste of time coming here to this crummy little rock! I told you we should have checked out Alpha Centauri instead.
Xynus: But maybe we can turn this “dud” into a success. What if we were to accelerate the evolution of life on this planet? Maybe we can turn a dull planet into something where intelligence might eventually evolve.
Zeesin: What do you have in mind? Finding some of those dismal organisms in this planet's oceans, and then gene-splicing them to soup up their evolution? That would be a pretty hard chore. You know I don't like to get my four feet wet.
Xynus: No, I have something very different in mind. We can create some species ourselves using our nanotechnology biology lab. We need merely specify some requirements, and the computer will take care of designing the appropriate DNA. We can print out the organisms cell layer by cell layer using our molecular materializer. Then we just dump the newly designed organisms into the oceans of this planet.
Zeesin: Okay, I guess there's nothing much else to do around here.

There are three ages in time when the idea of extraterrestrial intervention might be helpful. The first is the point when the most primitive life developed. Modern science has not yet explained a plausible scenario by which that occurred, partially because of the difficulty of explaining both the origin of a self-replicating molecule and the difficulty of explaining the origin of the genetic code. The second age in time is the Cambrian explosion mentioned here. The third age in time is the time when we saw the emergence of human intelligence. We might call this the “consciousness explosion,” when man seemed to gain in a relatively short span of time (geologically speaking) a variety of subtle mental characteristics such as aesthetic abilities, spirituality, math abilities, language abilities, musical abilities, introspection, and moral reasoning. Accounting for this consciousness explosion is perhaps more difficult than accounting for the Cambrian explosion, given that most of these things are not easy to explain through natural selection, as they are mostly not traits that increase an organism's likelihood of surviving until reproduction.

But there is a barrier to anyone suggesting that some design – either extraterrestrial or supernatural – may have played some role in the origin of life or earthly life or human life. Some scientists have declared that any mention of design in discussing such matters is “not part of science” or “unscientific.” This thought taboo is indefensible. A few examples show very clearly that there is no truth to the idea that “scientists don't consider the possibility of design” when trying to consider causes.

For example, imagine a strange radio signal is received from deep space. If the signal is sufficiently suspicious, a scientist will indeed consider the hypothesis that design was involved, and that the signal may be a signal from an extraterrestrial civilization. Or imagine that some suspicious looking structure (on an asteroid, moon, or planet) is photographed by a space probe. A scientist will indeed consider the hypothesis that design was involved, and that the structure may have been designed by some extraterrestrial expedition that arrived in our solar system. Or suppose a scientist finds some artificial-looking object buried in a geological bed. A scientist will indeed consider the hypothesis that design was involved, and that the structure may have been designed by some human or some extraterrestrial visitor. Any scientist could advance any of these ideas in a scientific paper without fear of being excluded because he had considered some possibility of design.

The notion, therefore, that considering (or arguing for) a possibility of design in discussing the origins of life on earth is unscientific (or not admissible in a science publication) makes no sense. Such claims need to be translated. When a scientist claims that a hypothesis is “not part of science,” what he typically means is that such a hypothesis “is forbidden or should be forbidden to scientists.” When he claims that a particular hypothesis is unscientific, what he typically means is that such a hypothesis is a taboo that violates the tribal norms of the scientific community. Such claims tell us about sociological and cultural restrictions and prohibitions within the scientific community, but usually don't give us any cogent principle as to how our thought should be limited.