The Book of Job, Revised

And it came to pass that a famous scientist came upon hard times. People called him names, women said he had castigated them unfairly, others questioned his sincerity. Some criticized him for speaking about things that he knew nothing of, and for even bullying children. He spoke to his friends and asked for their support. They agreed to support him. He said to them “Sometimes I wish there were a God, so I could curse him for the horrible world we live in and all the stupid people in it”. No sooner had he uttered these words, when the voice of the Lord began booming from heaven.

“Who is this that obscures my plans with words without knowledge?
Brace yourself like a man;
  I will question you, and you shall answer me.

 Where were you when I laid the earth’s foundation?
    Tell me, if you understand.*

Who brought about the fundamental explosion of all matter and energy?

Who allowed the forces of the universe to separate and become whole?

Where were you when I created gravity and set its constant to allow for a stable universe? When I made the hyper inflation? When I set up the constants for the strong and weak forces to allow for stars to form.

Were you present when matter aggregated and heated to form stars and later planets and moons?

Did you set up the chemical reactions in stars with the perfect resonance to create carbon?. Was it your idea that when stars exploded at the end of their time, all of their elements would seed planets with the material of life?

Have you formed the Earth with liquid water and a molten core, so that its rotation would create a magnetic field to deflect lethal solar radiation?

Did you create the moon to stabilize the Earth’s orbit?

Where were you when I brought forth life on Earth?

Do you know how the code in DNA was formed?

Were you there when I had the green plants use quantum physics to find a way to make food from sunlight?

Can you tell why all creatures evolve?

Was it you who got living cells to combine into large creatures?

What do you know about how I formed Humanity, so that you have a brain to think about my creation, and a voice to question me?

Have you ever given orders to the morning,
    or shown the dawn its place,”

The man listening to God’s voice said

“Surely I spoke of things I did not understand, things too wonderful for me to know.”

And for the first time, be began to pray for wisdom, knowledge and guidance, in the humility that underlies all of true science.

 

*All lines in  italics are from the actual Book of Job.

 

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Two new articles about the new evolutionary biology

My two related articles on the new evolutionary biology have come out at the same time:

Sy Garte “God and the New Evolutionary Biology” God & Nature Magazine Winter, 2016

and my first full original article in PSCF (at this time only available to ASA members)

Sy Garte “New Ideas in Evolutionary Biology: From NDMS to EES” Perspectives on Science and Christian Faith Volume 68, Number 1 pp3-11, March 2016

Comments on either article are welcome here or on the facebook group, Celebrating Creation by Natural Selection (CCNS) where I have also posted links to the papers. If you are interested in the PSCF article but cant get to it, let me know, and I can send you a pdf reprint.

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Deep in My Heart

Today’s post is nothing related to science. I did speak at my Church on Friday about humility, science and faith, and on Ash Wednesday went to an African American Church where I listened to their choir. That experience stimulated this post.

If religion was a thing that money could buy

The rich would live and the poor would die.

Those words are from a Negro spiritual, “All My Trials, Lord” and I learned them at the communist camp I attended back in 1957. I was ten, and didn’t understand the words at all. Religion is bad, so shouldn’t it be the other way around? The poor would live and the rich would die, must have been what they meant to say.

We learned a lot of Negro spirituals at that camp, along with union songs, anti-war songs, and songs about brotherhood and freedom. The spirituals were the most moving, but also made the least sense. They were all about God and Jesus.

Go tell it on the Mountain, over the hills and everywhere.

Go tell it on the Mountain that Jesus Christ is born.

And

I’m gonna walk with the Prince of Peace

Down by the riverside

 All those verses with Lord and God and biblical references, taught to a bunch of red diaper babies in a communist atheist camp – I didn’t get it.

I had learned the explanations: the Negroes were not really religious Christians, they were just pretending to be so they could survive slavery, and all those lyrics held hidden (completely nonreligious) meanings.

Or, alternatively, the poor, uneducated Negroes actually did believe in God, but it wasn’t their fault, since, well, they were poor and uneducated. We all knew that smart Negroes existed (I keep using Negro in this piece because that was the only acceptable term at the time. Black was still a decade away from replacing it.) Harry Belafonte’s son went to our camp, and there were one or two others. And of course there was Sidney Poitier.

Still, I remember being really bothered by all those times when we had to sound as if we actually believed in the absurdity of a magical sky fairy whenever we sang things like:

“All God’s children got shoes”  or “Do Lord, remember me” or “Oh sinner man, where you gonna run to?

And it didn’t matter how often I was told that when it came to religion, we had to give Negroes a pass. I just didn’t like it. The explanations didn’t ring true.

Of course, things got even worse soon. By the early 1960’s the movement had grown from sit-ins and school integration to marches and rallies. And there was no question where the leadership of this movement was coming from: the Black Christian Churches of the South. From Martin Luther King to Jesse Jackson, the strong leaders of civil rights were not politicians, not communists, not union leaders, but pastors. King’s speeches rang with the glory of God, and of Christ’s messages of equality and compassion, of love and charity. Now I was watching TV images of Black preachers exhorting Christian congregations to go out and join the struggle for freedom.

As the movement grew, many others joined in, but the most impressive, most powerful, most heart wrenching scenes were those of clergy – white and Black, Christians and Jews – who linked arms at the front of the marches and demonstrations as they faced the terrifying ranks of armed and brutal racists.

This was not the revolution I had been taught about, the one where workers overwhelmed the company thugs for the cause of economic justice and a living wage. This was a revolution where people of conscience were fighting to win the hearts and souls of their enemies in the name of love and Christian mercy. It was nonviolent by nature, something that Marx and Lenin never taught.

By the time I started marching in civil rights demonstrations, I was not a communist anymore, and I no longer found it quite so troubling to sing the songs of faith that had allowed a struggling people to endure. I had learned “We shall overcome” long before it had become the anthem of the movement.  When Dr. King gave his “I have a dream” speech in 1963, I no longer had a problem with the religious references.

Now that I am a Christian, I see clearly what I couldn’t see at the time, and everything makes perfect sense. I can now feel the presence of Christ in the trembling voices of the frightened kids as they faced fire hoses and baseball bats. I now understand the prayers of the handful of protestors, those desperate lonely witnesses to justice and dignity, who, despite all the odds against them, did in fact overcome. And when I recently heard a Black Church choir sing a hymn, with all the spirit and joy that I first heard 60 years ago, all of this came back to me, and I had to bow my head in prayer and thanksgiving for finally seeing the truth of how the Holy Spirit has always moved in the hearts of humanity.

 

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Former atheist astrophysicist, Sarah Salviander, explains her journey to Christianity.

I found this blog post and had to re blog it here, since her story is so close to mine. I was very moved to read it, and I simply had to share it.

 

James Bishop's avatarBishop's Encyclopedia of Religion, Society, and Philosophy

Screen Shot 2015-05-23 at 4.10.37 PM

Testimony of former atheist Sarah Salviander. She is a research scientist in astronomy and astrophysics at the University of Texas.

“I was born in the U.S., but grew up in Canada. My parents were socialists and political activists who thought British Columbia would be a better place for us to live, since it had the only socialist government in North America at the time. My parents were also atheists, though they eschewed that label in favor of “agnostic.” They were kind, loving, and moral, but religion played no part in my life. Instead, my childhood revolved around education, particularly science. I remember how important it was to my parents that my brother and I did well in school.

I grew up in the 1970s and 1980s, a time when science fiction was enjoying a renaissance, thanks largely to the popularity of Star Wars. I remember how fascinated I was by…

View original post 2,397 more words

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Thoughts On Evolution

Evolution is not simply change. Stars change, planets change, galaxies, mountains, rocks, and all aspects of the physical world change, but they do not evolve. Evolution implies more than simple change: it is an accumulating, progressive change that relies on the transmission of information from one state of matter to all future states. In life, this transmission of information is chemically mediated through the informational molecule of inheritance, DNA. Natural selection is the process that selects which states are most likely to pass their information, but without inheritance (a term that means the passing of information from one generation to the next) there is no evolution.

For example, if a cell were to develop a much better way to produce energy, it would prosper and probably fare better than any of its neighbors.  But if the new information about how to produce energy is not faithfully copied and transmitted to the next generation, there will be no accumulation of that new information and no evolution.

In living systems, this process of information transfer is highly robust and  leads to a steady, semi-irreversible accumulation of informational change. Robustness means that once a novel improved phenotype is produced, it doesn’t go away unless it is replaced by an even more improved phenotype. Without this stability, evolution would not work. This explains why some features of modern cells have not changed in billions of years: other features of modern life forms are continuously changing (body shape, organ physiology), but the more basic features are fixed.

We know of another form of evolution in the universe that behaves in a very similar way in that it involves passing down information to subsequent generations, but the mechanism of transmission is entirely different from what happens in biological evolution. I’m talking about human cultural evolution. Here the information that is passed from one generation to the next and that spreads throughout the population based on a form of selection is knowledge, carried by language.

In cultural evolution, the information transfer process has led to dramatic leaps of greater efficiency and accuracy of information processing leading to more rapid cultural evolution in a similar kind of positive feedback loop that we find in biological organisms. The steps involved for human cultural evolution are talking, memorization of verbal information, writing, printing, and more recently electronic information storage and transmission, most notably through the internet.

A clue to the similarity between biological and cultural evolution is the similarity in the shape of the curve of the relationship between time and change, or the rate of change function. In both cases, the rate of change began at a very low level, and then as improvements accumulated, including improvements in the evolutionary process, the rate began to accelerate exponentially. This is clear from any measurement of change rates in either model.

This coincidence points to a fundamental law of evolution that should apply to both biological and cultural evolution, defined as a progressive, accumulative (meaning mostly irreversible) process based on information transfer.

Evolution can be robust, progressive, and to a large extent irreversible, and still allow for – in fact require – extinctions. This includes things that might appear to violate the irreversibility rule, like loss of genes, or – on a phenotypic level – loss of limbs, sight, or any feature that improves the fitness of creatures living in a particular environment. So is the acquisition of limbs by land animals really irreversible if whales have lost those limbs? Yes, it is, because whales have not actually gone backwards – they have moved forward in a different direction based on a change in environment. Their limbs didn’t “devolve” back into fish fins, but  continued to evolve in a new direction. Even genetic losses are not really a reversible process, chemically speaking. Gene deletion is not the same as the reverse of gene formation – it is a forward moving evolutionary process that continues to be driven by natural selection.

What about the losses in cultural evolution? Think of all the dead languages, vanished cultures, forgotten technologies. Again, yes, extinctions are common, but the extinction of culture is not the reverse of its development – it is a change brought about by environmental conditions.

The progressive nature of biological evolution and cultural evolution does not mean that we can predict their direction, or that the direction of either is necessarily toward “good”, “better”, or even more complex But since selection is the rule in both cases, we can conclude that there are directions for biological evolution and cultural evolution and that innovation and increased adaptation to the environment will prevail. Overall, and with many exceptions, this also leads to an increase in the maximum degree of complexity at any one time. This doesn’t mean all organisms get more complex, or that all humans use more complex technology over time, but that the degree of complexity among some group of creatures does increase with time, and the complexity of the technology of some group of humans does likewise.

 

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An Important Book Review

The staff of Biologos asked me to review a new book by Discovery Institute’s Michael Denton. The book is called Evolution Still a Theory in Crisis, not an auspicious title for an evolutionist like me. But I read the book, and Im glad I did.

I think my review of the book (written with my wife and collaborator, Aniko Albert) along with an introduction by Jim Stump, Biologos Senior Editor, and a non technical summary by the Biologos Editorial Team could represent a turning point in the interactions between those who hold to Evolutionary Creationism, and some parts of the Intelligent Design movement.  I will repost the review here at a later date, but for now here is a link to the review and the other documents. Comments can be made here or there, as you wish.

 

 

 

 

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Free Will

The militant atheists I grew up with (my family and all their friends) considered free will a critical component of the human mind. The idea that people were to some degree free to choose their mode of action was crucial to the very fabric of liberal (not to mention radical) social action. The restriction of free will by outside agencies, like the Church, the oppressive ruling class, poverty, or lack of education, was in fact identified as the obvious enemy of progress.

Modern militant atheists, on the other hand, now hold that outside agencies do indeed have such a strong influence on our choices that free will does not exist. For some time I have been puzzled by this assertion, not only by its counterintuitive nature, but also why this idea would be a bedrock of atheism.

Sam Harris, one of the more influential New Atheists, has written a book and given quite a few talks on this subject. According to Harris, the illusion of free will is closely related to another idea popular in the atheist camp; namely, that consciousness is also an illusion. This makes some internal logical sense, since if we have no real consciousness, we cannot make conscious choices.

But the heart of the matter about free will is determinism. Harris believes in a universe where everything that happens has a series of causes and that there is no way to avoid obeying those causes.

“We live in a world of cause and effect…Either our wills are determined by a long chain of prior causes…or they’re determined by some random influences…and consciousness is clearly not in the driver’s seat.”

Sam Harris

If you decide to visit your friend, and you do so, it wasn’t your choice, but the unalterable result of all of the billions of events that led up to your illusory decision. You had no choice, just as the snow has no choice about whether it will cascade down the mountain in an avalanche.

So Harris and the atheists see us (and all other creatures, of course) as nothing more than automatons acting in accordance with all of the physical and chemical influences that impinge upon us.

This is based on a 19th century view of reality, though then, it was only understood to apply to the physical universe, not to the lives of humans. It harkens back to the Clockwork Universe model of the world, where all events are predictable, given enough information. It ignores all of science from the 1920s on, including quantum uncertainty (which is absolutely nondeterministic), as well as deterministic chaos, the new laws of complexity, and just about everything we are learning about how particles, atoms, and biochemical pathways are dependent on random events. Even pure genetic determinism (Richard Dawkins’ contribution to this mess) has now gone out of favor with evolutionary biologists.

Of course, it also ignores the reality of human experience, while it is again logically consistent with the New Atheist view that human beings are really nothing more than slightly more complicated earthworms.

What an incredibly depressing and bleak philosophy modern atheism has become. To hold that human consciousness and human free will are not real, but only evolutionary spandrels that help us cope with our huge brains; to profess that we are all slaves to a purely deterministic past and have no control over anything; and to conclude that human beings, like the universe, are devoid of purpose or meaning – all this used to be called nihilism, and was not very popular at the time. For obvious reasons.

I feel sorry for the New Atheists. But I feel even sorrier for their children. Anti-theists like to claim that teaching children about God is child abuse. It seems to me that teaching children that they are purposeless, meaningless robots, without the ability to make their own decisions or even think their own thoughts, is far more abusive.

And I will end by saying that I decided to post this of my own free will.

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STOP signs

Several decades ago, I was driving along a country road looking for a cabin owned by a friend of mine. The directions he had given me were vague at best. I came to a spot where the very rustic road vanished completely. I saw an old sign that read:

“STOP! NO MOTOR VEHICLES BEYOND THIS POINT.”

I sort of parked the car, and proceeded to walk along a well-marked foot path a couple of dozen yards to a clearing, where I could see the cabin in the distance.

I had been somewhat annoyed when I started walking, since I had a lot of gear in the car I would need to haul to the cabin, but I soon got over it, and for the week I stayed there, I came to appreciate the total silence and solitude that came with being “off road”.

When it comes to knowledge we have become used to a certain way of moving forward. We have the smooth, well-paved road of science, which many think can go everywhere we might want to visit. We travel down that road on our conveyances of rational induction, objective reproducibility, and other vehicles mass-produced by the Scientific Method Transportation Co. And we almost always get where we want to go, or at least where the road takes us.

But almost always is not always. There are a few roads in our scientific universe that also have STOP signs. Signs that say “Go no further in your vehicle.” In order to continue we need to dismount, and go on foot, or with some other kind of conveyance.

This is not a popular idea among some modern atheists – those who subscribe to a view that many theists call scientism. One definition of scientism could be the belief that such STOP signs do not exist and cannot exist, that everything we ever might want or need to know about anything can be achieved with the scientific method, and only with the scientific method.

I once had a strange conversation with a scientism-believing atheist about how we could possibly evaluate the quality of art using objective, scientific criteria. He informed me that it was easy – in order to get a good quantitative measure of the artistic value of a painting, simply find out its current market price and compare it to the average market value of other paintings. He was serious.

In fact, it isn’t only art, values, and philosophical ideas that resist scientism. Most importantly, science itself proves its falsity. Physics has told us that there are some things we cannot know: there are STOP signs we cannot pass using science. The position of an electron cannot be known at the same time as its momentum, ever, anywhere, by anyone. The Uncertainty Principle is not in place because we need to do more research; it’s the result of research and it won’t change.

Just recently another unexpected STOP sign showed up in physics. A paper in Nature called “Undecidability of the Spectral Gap” proved mathematically that it is sometimes impossible to determine the properties of the energy difference between the ground state and first excited state of a system, which is called the spectral gap. I don’t know nearly enough physics to be able to understand what this means, but I think I understand the basic conclusion of the paper: “Our result implies that there exists no algorithm to determine whether an arbitrary model is gapped or gapless…”

So we now have an undecidability issue, along with an uncertainty principle and Gödel’s incompleteness theorem in mathematics. All of this is strictly within science. None of this is unexpected – scientists have always known that there must be limits to how far they can go in understanding all aspects of reality (see my previous post about constants). Science is often unable to address ‘why’ questions, especially those associated with human emotions and purpose. I think that as we go further in biology we will come across a few STOP signs also. There are some aspects of cellular biology that are starting to look as complex as quantum mechanics.

So the question is, if and when we come to a STOP sign and can go no further in our scientific-rational-materialism vehicles, should we still try to make progress? If we don’t want to give up and say “Well, we can go no further with science, so we’ll just turn around and go home”, then how do we proceed? What kind of vehicle should we find? I don’t know the answer, but I do know there are a lot of options. We can try the bicycle of philosophy, the skateboard of psychology, or sometimes we might want to use the moped of theology. I would say whatever works is worth a try, even if it means striking out on foot, with whatever crazy, personal, brand new idea that nobody has ever thought of in our backpack. We might not get there, but the trip is worth the effort. And who knows what we will find past the STOP sign.

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Gene Regulatory Networks

Gene Networks are collections of genes that interact with each other. What does that mean, and how do genes interact?

First, we must understand that a gene does nothing but store information. The analogy most often used is a book. A closed book is of no particular interest or value, and many genes are in fact usually “closed” or turned off. What that means in biochemical terms is that the transcription process in which the sequence of bases in the DNA is converted into a matching sequence in RNA (which then goes to a protein-making factory called the ribosome) does not happen. So when a gene is turned off, the information in the gene is not expressed, and the protein that the gene codes for is not made. The gene is inactive. The book is closed, and the information that it contains (in the case of genes, the protein the gene codes for) isn’t needed.

But then something changes. A toxic material enters the cell, or a lot of energy is suddenly needed,- or the cell begins to divide because it has grown a lot. In the analogy,  we might remember that the recipe for how to make chicken soup is in a cookbook, so we open the book and find the information we need. In cells, when a particular protein is needed, a signal goes to the gene that makes the protein, and the gene is turned on, activated, transcribed, expressed (all synonyms for the same thing). And the process starts.

Enzymes and other proteins copy the DNA of the appropriate gene into RNA, which is then translated into a protein sequence by an incredible process in the ribosome. This is  what we do when we read the words “Cut the chicken into small pieces” in the cookbook. Those words are simply marks of ink on paper, but they are in a language that we can understand and translate into a meaningful idea. The process of protein synthesis is technically called translation, and the analogy is a very good one.

The way genes are turned on and off has been an active field of biological research for many decades. It is a very difficult field since the mechanisms are diverse, complex and hard to untangle. What we are finding is that the entire subject of gene regulation is probably far more important in all aspects of biology (including evolution) than we ever suspected. Recent research has shown that many DNA regions that were not recognized as genes actually code for proteins whose only function is to regulate other genes.

Even more fascinating is the burgeoning field of gene regulatory networks, where groups of genes regulate (or control, like switches) each other. These networks (GRNs) are very important during animal development: they are responsible for how the growing animal develops organs, limbs, and all the structures that make it what it is.

Studies on GRNs have shown that they are very stable over deep evolutionary time, and some of the key genes involved in these networks during development have not changed much in hundreds of millions of years of evolution. The complexity of GRNs includes several kinds of feedback and redundancy features that reduce the chances of disruption by mutations or random cellular events that could affect normal function. This resistance to damaging disruption is called robustness or gene buffering. At the same time, and probably as a consequence of this robustness, these networks can be a source of innovation in evolution.

One of the pioneers in theoretical modeling of GRNs is Andreas Wagner, whose book The Arrival of the Fittest presents many of his ideas about how gene regulation could impact the process of evolution, especially as related to mechanisms for variation that are outside of the standard neo-Darwinian paradigm.

I have also been working with models of such networks for the past few months in order to try to understand some of the basic dynamics and mathematical relationships that govern their behavior. This work has been funded by the John Templeton Foundation (see the page on the John Templeton Foundation grant). I am finding the work to be fun and exciting, and I am getting close to some interesting findings. But I don’t want to discuss those finding here and now (they are much too technical for this blog). What I want to do is say something about the philosophical implications of interactive networks.

The models I am using are simple mathematical matrices where each element can have an effect on every other element of the matrix. This is not at all specific to gene regulation but also applies to a large variety of systems. Probably most systems, in fact. Certainly it applies to human interactions in many ways. It’s reasonable to postulate that any group of humans constitute an interactive network. Even in small groups, like families or friends or co-workers, the complexity of these interactions and their results are beyond calculation. Like all systems that exhibit highly complex non-predictable behavior (the weather, stock market, so many other chaotic systems), interactive systems are deterministic, and end results could theoretically be calculated if one were able to have knowledge of all the parameters of the system. In other words, if you know that Uncle Jerry has no respect for his son-in-law, and that your mom is always striving for peace in the family, you might think you would be able to predict certain scenarios during Thanksgiving dinner. But you would not be able to predict that your sister’s new boyfriend would argue with Uncle Jerry all night, and even convince him that the Red Sox will never win another world Series.

It’s no surprise that gene regulatory network models (with very simple kinds of interactions) can get extremely complex, to the point of this kind of chaotic, unpredictable behavior. Wagner has published this result.  What is surprising (and this is a preview of some of my results) is that this level of complexity begins to show up at some of the simplest networks with very few interactions.

Is this complexity a good thing? It might be that it is for biological systems. The brain is probably the most complex thing in the universe, and it’s a pretty powerful thing indeed.  Some of the biochemical machinery that functions  even in primitive cells (like how proteins are made from the DNA-based genetic code) are complex beyond our comprehension, let alone ability to imagine how they got that way. So yes, complexity seems to be the rule in life, and evolution seems to favor it whenever possible. This is not a new insight by any means, but it is something that leads to many interesting questions for our incredibly complex minds to ponder.

 

 

 

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It’s Only Logical

The true function of logic…as applied to matters of experience…is analytic rather than constructive; taken a priori, it shows the possibility of hitherto unsuspected alternatives more often than the impossibility of alternatives which seemed prima facie possible. Thus, while it liberates imagination as to what the world may be, it refuses to legislate as to what the world is.”

Bertrand Russell

 I love logic. One of the few free electives I took in college was symbolic logic, which became one of my favorite courses. What I learned is that logic is a fun way to do math and prove or disprove textual statements. But most people misunderstand what logic is and how it is used, and, more importantly, what it cannot do. As Russell (who knew more about logic than anyone) says, “…it refuses to legislate as to what the world is”. In other words, logic ain’t science.

It’s true that logic was at one time the language of what passed for science, but that time has long gone. Contrary to the ideas of Aristotle and the wisdom of the ancient Greeks, truth cannot be grasped by the application of logic. In fact it is only in very limited circumstances, mostly related to mathematical proofs of theorems, that logic is a useful path to truth.

One of the premier principles of logic is that what it is designed to determine is not truth, but validity. Any system of logic is based on the discovery of theorems that are derived from basic premises. Some of the premises are self-evident, or assumed to be true based on universal experience. Proofs are only as valid as the truth of their premises. Once we leave the rarefied territory of pure math and symbolic logic, premise truth becomes a serious issue of concern.

Even when we have 2 or more true premises, the ability to draw a true conclusion from them requires the strict following of a set of rules. In formal logic it isn’t enough to list the premises and the conclusion; you must also specify by which rule the conclusion follows the premises. For example

  1. If a man is tall, he can reach the top shelf.
  2. I cannot reach the top shelf.

Therefore I am not tall, by Modus Tollens (If A, then B. Not B. Therefore Not A).

That is a logically true statement. The second premise might be false (maybe I am lying about not being able to reach the top shelf), but the proof is still valid, even if not guaranteed to be true.

However, if I used the same two premises and then concluded that no woman can reach the top shelf, the argument would be fallacious, because such a conclusion is not based on either of the premises, and there is no rule (there are 19 altogether) that allows such a conclusion from those premises.

What logic can do is determine the likely truth of a theorem assuming that the underlying premises are known to be true. But logical systems cannot, and are not meant to, deal with the underlying truth of a proposition.

The major contribution of the thought of Francis Bacon, and of all the inductive reasoning from Galileo on, was that the truth of basic propositions can be determined not by logic but by experiment and observation. This was the beginning of a new philosophical way of seeing the world, and it would be eventually called science.

We now know that there are scientific laws and truths about the universe that defy logic, Natural law can only be discovered by observation of, and experimentation with, the natural world as it is.

Is it logical that it is impossible to know the position and the momentum of a photon at the same time? No, but it’s true. Is it logical that that the universe started out as a singularity which was also the beginning of time? No, but that’s true too. How about the fundamental logic of the fact that a wave function for the probable state of a particle collapses to a particular value only when observed? True, but not at all logical as we generally use the term.

Biology is worse. A great deal of biological reality cannot be reduced to logic, even though we know a great deal of the truth about how cells function. It isn’t terribly logical to have so much unused DNA in cells that must get copied over and over again. (And no, the idea that all of the DNA is used is wrong. It was an awkward error by the ENCODE group.) It isn’t logical that genes are broken up by exons or contain so many transposons, or that humans lost so many genes for smell.

But there is a good side to the illogic of biology and physics and all other sciences. It means we are always being surprised by what we find out – it’s usually not at all what we expected. We have the powerful method of science to discover truth about our natural world, and it’s up to us to make sense of our findings, whether they are logical or not.

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