Simply Simon

I have posted this before.

Today is simply Saturday,  the day between. We know very little about what happened on this day, but we can imagine.  We can imagine a man, much like us. A man defeated, alone, miserable and afraid. This man, who was once called a rock, today thinks of himself as simply – Simon. Imagine him sitting in a strange house in a city not his own, staring out the window, seeing nothing but his own failure, and the loss of all of his hopes and dreams. I have felt this way at times, and perhaps you have also.

He thinks of the glorious promise that he has witnessed the past months, the miraculous and wonderful things he has seen and heard. He thinks of the Man who showed so much faith in him, the Man who has now gone, died, left them all alone, without hope or will. But most of all he thinks of his own terrible failure and betrayal. A failure that his leader had predicted, and which he himself would never have imagined possible.

Yesterday, that black day, had proven to the man once called the rock, that he was made of no more than weak, mortal, human clay. Three times he had confirmed his human cowardice, his unworthiness to lead, or even to live. On this Saturday, the man who now once again thinks of himself simply as Simon, is filled with an unimaginable despair at the loss of everything he once valued, most especially his own dignity.

Have you  been there? Have you had to face the fact that you are unworthy because of your actions? No excuses, you simply failed. The time for heroism, for standing tall, for being more than you thought you could be, the time to prove yourself truly a rock of faith, of hope, of goodness, the time had come, and you…you had failed to heed the call. In your weakness or fear, you had simply turned away, waving your hand in dismissal. “No” you said “I don’t know anything about that, Leave me alone”. And not just once, but often. And then it was over, the terrible moment passed, and you were left with only the taste of the ashes of your own personal failure, as the whole glorious edifice you believed in and had worked so hard for, came crashing down in chaos and defeat.

I have been there. That is why I have long been so fascinated by this day without a name, that lies between the day of anguish and the day of triumph. On this day, Simon sits in agony and stares, not yet knowing that tomorrow everything will change again. Today, he is still unaware of tomorrow’s miracle that will change everything in the world forever. Today is the lowest point in his life, but tomorrow he, along with his dispersed friends, will be witness to a breathtaking renewal of hope. The resurrection of tomorrow means not only the resurrection of the living God, not only the rising of the Son of Man, but also the rising of man himself. A man like Simon, weak, afraid, defeated, failed, a man whose despicable actions on the Friday have left him hopeless and full of self-loathing, also rises on Easter Sunday, and once more becomes Peter the Rock.

Like us he is all too human, and yet like us, he is capable of all that he later accomplished. I do not believe he ever forgot his acts of betrayal. But through grace and faith, and his human moral strength, he rose above them, and he fulfilled his destiny as a great fisher of men. So of all the miracles of tomorrow and the days and years that follow, for me the greatest is the miracle of the redemption of the man – the mortal, ordinary fisherman named simply, Simon.  Peace be with you on this day.

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A Very Old Story

One day, 12,494 years ago, somewhere in the middle of Mesopotamia, a young woman named Maya (I don’t know if that was really her name, but I like it, and it does have an Ancient Near Eastern ring to it) was walking around her village feeling bored. She had plenty to do, taking care of three babies and a couple of toddlers, gathering wild grains and nuts, washing clothes and sweeping out the hut, talking to her sisters and aunts and neighbors, and so on. But all of that was just…. boring.

Her husband, like all the rest of the guys, was out on one of their interminable “hunting” trips. She had no idea why they had to spend weeks wandering around and then come home with a couple of deer and some rabbits that they could have caught in a day or so. Well, of course “having no idea” was sarcasm, she (and all the other women) knew exactly what they were doing. Oh yeah, they did do a little hunting, but a lot more drinking fermented fruit juice, and maybe some visits to those harlots in the next valley, and a lot of stupid, drunken singing and storytelling. Men.

Poor Maya was, although she didn’t realize it, one of the smartest human beings alive at the time (or ever for that matter) and she was just bored and frustrated. The only person she could really talk to was the Shaman, who was smarter than most, but he almost never knew the answers to her questions, other than to say “It’s magic.” She wanted to know why the lightning and the thunder arrived together, but the lightning always first. She wanted to know why dogs seemed so smart but couldn’t talk. What happened after you died? What was the moon, and why did it move? And so on. The Shaman would look at her, smile and shake his head. He was in charge of making the rain stop, getting people better when they fell sick, and telling everyone what their dreams meant. But he only knew what he knew, and all of that was magic.

On this day, feeling bored, Maya, holding one baby on her hip, and taking a toddler by the hand, wandered over to a flat patch of ground just outside the village, before the forest started, where a couple of weeks ago she had done something silly. Last year, having noticed that wild wheat grew from the ground, she had taken some wheat and buried it in the ground, just to see what would happen. She wondered if it would pop up again. It did. She told everyone, and the general reaction was disbelief or disinterest. But two weeks ago, she had done something a bit different. She had seen many times how the tiny hard seeds (they weren’t called seeds yet) of many plants, even trees, flew around the air and finally settled in the ground. So this time she had buried only the seeds of the wheat.

When she got to her patch (the very first garden or farm, ever), there were the shoots sprouting from the ground. Maya was no longer bored.

The council meeting (composed of all the men) agreed to hear Maya, and they all laughed at the folly of women. Nobody believed her trick, and as one wit put it, even if it were true, so what? But the Shaman and the Chief were lost in thought and didn’t laugh. The Chief asked her, “Can you eat the wheat that grew from those seeds?” “Yes,” she said, “I used it making bread.”

“Hmm” said the Chief, who would become the world’s first economist.

“But how is such magic possible?” asked the Shaman. “You are saying that you have made something from nothing. How can a whole plant come from a tiny little stone? It makes no sense.”

“How does a baby come from the seed of a man?” Maya countered (I told you she was a smart cookie). The people were not completely sure that this was true, but Maya was, because she had done a careful epidemiological study. Women only became pregnant if they had sex.

So, that was the start of the revolution in human life that led in a direct line to shopping malls, reality TV, the internet, and all the other manifestations of the fact that human beings have too much free time on their hands since food is so easy to come by.

So what is the answer to Maya’s question about seeds and plants and babies, and in fact all of her other questions? We know of three ways to answer all questions. Magic, religion, and science. Magic came first and is the most primitive and least useful. Magic is a chaotic system with few if any rules, and it presupposes a universe filled with capricious and unpredictable spirits, demons, demigods, and mysterious forces which make things happen that have no explanation. According to magic, the spirit dwelling in the seed comes forth to make a plant. This spirit could decide, however, to not show up, or just sleep through the season and allow a famine.

The twin children of magic are religion and science. No, religion is not the same thing as magic. Religion (like science) is based on overarching principles and the concept of an order in nature that cannot be violated by spirits, demons, or humans. The religious idea of agriculture is that God made plants and animals, and the creation of plants included the wondrous properties of their seeds to produce bounty for humanity.

Science also uses some all-encompassing ideas and techniques to find out all that is possible to learn about how things happen. Scientific investigation allows us to probe quite deeply into the mechanisms by which seeds produce plants, and the information we learn is so astounding that it leads to ever more questions.

Maya knew all of this already 12,494 years ago. She believed in a God who oversaw everything that happened. She also believed in the spirits of the woods, and the earth. And she believed that she could find truth by paying close attention to the world around her, and by trying things out to see what happened. With time, God and reason made the spirits unnecessary and inconvenient for humans to still believe in (although magic is far from dead in the world). Many people today believe that God and science are engaged in an epic struggle for supremacy, but the reality is that both are needed. But that’s a whole nother story.

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Morality and Evolution

There is of course, no question that genes play a role in behavior throughout evolutionary history. Bees, for example are known to sacrifice their lives for the good of the hive. But while this might appear to be the result of a laudatory impulse on the part of individual bees, it is nothing of the sort. No bee decides, in a moment of supreme valor, to give her life for the good of her fellow creatures. There is no moral imperative acting here, but only the evolutionary pressure that produces an appearance of high altruism. Clearly no virus ever decides to be “good” and target the upper respiratory tract rather than the lungs. Increased transmissibility and decreased host mortality is a well known and very frequent evolutionary strategy for infectious, lethal viruses.

While these are fairly extreme examples, the same sort of thing applies to a large extent (though admittedly not entirely) to behavioral traits coded for by human (as well as other animal) genes. Increased empathy might be expected to result in behaviors that are more “morally good” according to many human cultures. But a careful examination of the literature shows this is not always the case. Genetically determined autonomic reactions to a scene of violence may lead to complex and variable behavioral outcomes. This point is made in several papers that reference the OXTR rs53576 allele of the oxytocin receptor gene, one of the most studied behavioral genes. .

Even if there were a much tighter relationship between phenotypic effects of genes related to feelings and emotions with behavioral consequences, it is very well known that both emotions and behaviors are multigenic, and often involve highly complex gene environment interactions. A large literature of identical twin studies has shown that genetics accounts for no more that 50% of almost all behavioral and mental phenotypes. All of this makes prediction of anything to do with moral actions based on genotypes of one or a few genes extremely difficult.

Taking the OXTR allele as an example of this complexity, we find that in a paper describing the effects of the gene on empathy, the A allele appears to be dominant, whereas another paper, finds the G allele to be dominant  for effects on child behavior.

Both studies concur that this polymorphism is in Hardy Weinberg equilibrium, meaning that selection pressure for either allele is currently absent, and the gene probably was never a target for natural selection.

Returning to the issue of moral choices, the very fact that there is no single objective morality for all human cultures is strong evidence against an evolutionary genetic connection. Yes, there are differences in allele frequencies in many of these genes in different ethnic groups, but these differences are generally not meaningful. I was once involved in the review of a grant application which hypothesized that different frequencies of a particular polymorphism in a neurotransmitter gene could explain why African Americans are more violent than European Americans. The grant was not well received due to lack of any preliminary evidence and the implausibility of the claim. The truth is that human populations differ genetically from each other only in very small ways, and social, cultural and psychological factors far outweigh genetic factors in determining moral and ethical behaviors.

This does not mean that there are no genetic correlates with human acts of moral good or evil. All humans (except for rare variants like psychopaths) recognize the inherent good in caring for children, in love, and in doing kindness to kin and relatives. And all recognize that doing harm to these people is bad. There is no question that these moral understandings and resulting behaviors are of evolutionary origin, since the same behaviors are seen in many mammalian and even other animal species.

But we only need to think of moral values in modern cultures that extol the killing of “enemies”, the mistreatment of people with sexual or other nonconforming phenotypes, the way women are treated and so on, to see that once we go deeper than the fundamental common values, we find purely cultural determinants of morality, with no genetic influence at all.

Cultural evolution (which includes good explanations for different human moral codes) is fundamentally different than biological evolution, which depends on genetic variation. For morality it is memes, not genes that count. It is cultural evolution, not Darwinian biological evolution that has given us fire, shelter, technology,  the internet and everything else that makes us more than just another ape.

Links to the papers mentioned:

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The Good Old Days

Everyone knows how horrible modern life is, especially here in the US. Technology running rampant, terrible food, crowds, pollution, on and on. If only we could turn the clock back and live like we used to in “The Good Old Days”

The Good Old Days were really great. Think about how well we used to eat. No preservatives, no chemical additives, just pure, unadulterated, partly spoiled meat, fish and dairy products. Sour milk has now become a lost food item, that most of us (except for a few single guys who insist on drinking week old milk straight out of the carton) have never even tasted. And we didn’t have to worry about fruits or vegetables going bad because there weren’t any, unless you lived in the country.

And no junk food!!

So wait, you are asking, if people didn’t eat Snickers, Cheetos, meat, milk, fruit, vegetables, what DID they eat? Bread, mostly. Good nutritious, whole grain bread. Morning, noon and night. Some folks had corn, tomatoes and potatoes also. Lots and lots of potatoes.  Of course this was true in the more recent Good Old Days, since corn, potatoes, tomatoes, and other crops (chocolate, tobacco) didn’t exist in Europe until they were brought from the New World.

The Good Old Days were really good old days when it came to beverages. None of this modern nonsense about drinking water. Ground water, (rivers and streams) was too polluted to drink in the good old days, so unless you had a well, water was not an option. Even wells often went bad, and people learned to only accept water from trustworthy sources. Milk was also not an option, unless you were on a farm. Juice and soda didn’t exist. (no fruit, remember), and coffee was a rare luxury. Tea was available, but could be expensive (remember the Boston party?).

So people drank what was safe, – alcohol. That why they call it the Good Old Days. Beer, mead, ale, wine, this is what everyone drank all the time in the Good Old Days. Drinks with alcohol were safe from bacterial contamination, and besides had many other advantages. They made the idea of spending 13 to 16 hours a day working in a field, or in a mill, or just trying to survive, a bit more palatable. After all, we should remember that in the Good Old Days, 99% of folks were poor.

And being poor in The Good Old Days meant being really poor. No spoiled kids crying because they didn’t get a Wii for Christmas. No kids crying because they didn’t want to go to school. No school. Nobody complaining about waiting at the doctor’s office for an hour. No doctors. With an average lifespan of 35-45 years, the whole problem of taking care of old folks, and what to do after retirement just didn’t  come up.

Also, that whole conflict that women face these days about choosing between career or family, well, that wasn’t an issue at all in the Good Old Days. Women got married, had kids and raised them (or the few that survived infancy), until they died in childbirth or from starvation or plague. Ah the simple life, free of those tough decisions we face these days. Well, actually, sometimes women did have choices to make, If she failed to find a husband, or if her husband died in a mill, mine, farm or other accident (or was killed in a war, or by a thief or a nobleman). a woman had the choice of prostitution or the convent. 

Now you might be starting to think that I am being sarcastic, and that I hold the view that Good Old Days were really pretty crappy. There might be some truth to that. My problem is that I can never really figure out exactly when and where the Good Old Days were supposed to have taken place. A time and place that we would all love to return to. At the moment Im stumped. I did have a nice day yesterday though.

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During my scientific research career, I have never known of any scientific field that is not marked by controversy. When I retired from research and took a position as a senior official in the Center for Scientific Review of the NIH (the agency responsible for managing the review of 80% of US grants in the Biomedical sciences), this observation was strongly confirmed. In many study sections, controversial ideas were often hotly debated.

Controversy is part of the scientific process and is often the driver of progress. New ideas, which are the fuel of science, are always controversial, until sufficient evidence is accumulated for them to attract support. The worst thing that can happen to any area of scientific research (as I have witnessed) is an end to controversy. The development of a profound and stifling consensus is usually the signal for a stagnant and soon to be outdated field.

As Christian scientists or Christians interested in science, how should we deal with scientific controversy? There are those who propose we avoid it. They claim that the entire movement of evolutionary creation, theistic evolution (TE/EC), is based on the premise that Christians should strictly adhere to the consensus views of mainstream science, and reject the controversial positions associated with pseudoscience, such as young earth creationism, or intelligent design. I agree, of course. Being a Christian should not give us warrant to reject sound scientific principles.

But how far should this go? Do we avoid all scientific positions that seem to be held by a minority of scientists at the moment, for fear of being labelled “unscientific” or apologists for a “Christian-friendly” approach to some issue? Some within the TE/EC movement would say yes. Many of these people are not scientists themselves, or have not been active researchers, and their focus is not on finding new (and therefore controversial) truths about the world, but rather on teaching known truths and agreed upon consensus views to other Christians. Their goal is to foster a tolerance from the wider scientific community by avoidance of any boat rocking that might cast doubt on the legitimacy of their claims to be followers of science. I think there is a role for this attitude, and it is a proper and important part of the overall mission to advance the cause of Christ in the world we live in.

But it is not the only such mission for Christian men and women of science. Some of us want to go further. Some few may take the risks that all good scientists take to stir up controversy, to propose bold new ideas, to do the work needed to support those ideas, argue for them, provide data for them, and not worry if they are outside the mainstream, in fact deliberately go outside the mainstream.

And when we do that, we should pray for support, not antagonism from our fellow Christian scientists in the teaching and outreach camp. Because, when we do this sort of work, or when we proclaim and support such work done by others, we are doing two things: we are behaving in the best traditions of pure science, and we are helping to advance our knowledge of the truth. If we act according to the rules and procedures of strict scientific rigor, we need not worry about the consequences of our actions, since in both science and faith, God’s truth will always prevail.  ‘

I was recently appointed to the editorial board of a new scientific journal called BioCosmos . The journal’s mission is “to present a wide variety of novel perspectives on the origins and nature of life that go beyond the standard neo-Darwinian paradigm of biological evolution. The focus will be on theoretically innovative, data-driven analysis and experimental results from biology and biochemistry… The aim is to encourage high quality scientific research and debate, which result in novel theoretical or experimental approaches that deal with unsolved problems of the standard biological theories. “

At this point, reading behind the lines, you might have the impression that this will be a journal focussing on Intelligent Design or other non-standard views of biological evolution. You would not be entirely wrong, but I think there is more to it than that.

The next part of the mission statement says “the journal’s peer review process will take to heart Newton’s ‘Hypotheses non fingo’. In other words, it will judge the theoretical claims proposed by authors in terms of the evidence placed before the reader rather than in terms of how standard theorists might deal with the same evidence.”

In two Zoom meetings of the Editorial Board, the issue of what to include, and whether to automatically reject certain topics was discussed. There emerged a consensus that the main criterion for paper acceptance in the journal will be scientific integrity and and the quality of the data, discussion and interpretation of results, as in any other mainstream scientific journal. It was also agreed that purely philosophical papers would be better placed elsewhere. What will not be part of the review process is avoidance of controversy.

All members of the Editorial Board see this as an experiemnt and an adventure that may or may not succeed. At the moment there is only one paper that has been published and appears on the journal website, which happens to be my own. The paper went through 2 rounds of rigorous peer review,  and I would assume that will be the norm. A couple of other papers have been accepted, and eleven have been rejected.

The true test will come when a scientifically unimpeachable paper presents some controversial views. Hopefully, this new journal will survive and provide a respected platform for the kind of good scientific work that many in the Christian and science community want to do, as discussed above. Prayers are welcome.

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THEM (A Confession)

Early one morning a few years ago, a nondescript man started on a journey to a foreign land. The man was dressed casually, and inexpensively, He carried an ordinary briefcase filled with secret papers. He passed unnoticed through airport security and customs. At his destination he was met by a special unmarked van. Besides the driver, the vehicle contained three of his compatriots, all heading to the same private meeting. He knew two of the passengers, one well, the other only casually. He didn’t know the third man, but he had heard of his reputation. Like himself, his fellow passengers in the van appeared ordinary, and no one would have guessed that each of them was in control of millions of dollars, euros or yen, and headed large teams of associates. They were all in their 50s or 60s and had become powerful leaders at their local bases of operations.

The van deposited them at a small rural resort that was to host this international powwow of about 70 such men and women. There was no security because this meeting was so secret, so unknown, that none was needed. There were no cameras, no press, no tourists, no outsiders. Few other people in the entire world knew that this meeting was even taking place, and they were not talking.

At the meeting the nondescript man listened carefully as the discussions and presentations of his fellow conspirators wove a complex thread of potential collaborations, financial management, and distribution of resources. Reports of progress, intelligence on issues of import were shared among all the participants. And then, of course, there were the private, even more secret, hallway tete-a-tetes between pairs and small groups of individuals, all designed to further the individual ambitions of each of the conspirators, while also moving their common agenda forward.

They naturally all knew that their discussions and decisions would have a major impact on the lives of millions of people all over the world. They laughed and joked, just like any ordinary social group would do, but behind their sometimes casual and jocular behavior, the seriousness and indeed fanaticism of their common goals was always present.

It sounds pretty ominous. And it is all true. I know  because I was there. Yes, I am the nondescript man, one of the conspirators at this secret, totally unreported, never publicly discussed meeting in the quiet secluded mountains of a foreign country. I confess. I am one of THEM.

So who were we, and what were we discussing? Care to guess? I will give the answer in a comment later.

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Claims and Evidence

A claim is an assertion that something is a fact. “The world is round” is a claim. So is “the moon is made of cheese,” “the genetic material is composed of DNA,” and “the gravitational force applies equally at all scales of mass.”

Other than the one about the moon, all the above claims are based on evidence. Let’s look at some of the scientific examples.

When the claim that DNA was the molecule that governed inheritance was first put forward as a hypothesis, it was roundly rejected by the great majority of scientists, partly because of a lack of evidence, but mostly because it appeared to be entirely implausible. Arguments against DNA were focused on the fact that almost everything that happens in cells had been demonstrated to be mediated by protein enzymes. No one thought there was any reason why this should not also include genes.

Then in the 1940s, a scientist named Oswald Avery showed in experiments that it was the nucleic acid fraction of cells, and not the protein fraction, that was carrying the genetic information from cells to their offspring, at least in bacteria. This new evidence elevated the claim to some extent, but it was still not at all universally accepted, because of the continued sense of implausibility. How could the relatively simple DNA molecule (simple in the sense of being composed of only a few chemical components) encode complex information? The answer might lie in the details of the long polymeric structure of DNA, but nobody knew anything about it back then. And that’s where Watson and Crick came in. Their solution to the structure immediately showed that it was the sequence of the bases, and not simply their composition, that was the key to how genes worked. Now the plausibility of the claim being true became so much higher, and combined with Avery’s evidence and the evidence from later experiments, it was finally accepted that DNA is the genetic molecule.

Another way to frame a claim with no evidence and very low plausibility is to call it an extraordinary claim. Such claims are fairly common in science, especially if we include brand new ideas in the category of low plausibility. But the idea that such claims require “extraordinary” evidence to be considered true is wrong. There is in fact no such thing as extraordinary evidence. The term does not appear in the scientific literature. There is weak evidence and strong evidence, and they have nothing to do with the strength (or plausibility) of the claim. Less plausible claims might require stronger evidence to be believed than more plausible claims, but even weak evidence will immediately increase the plausibility of the claim, so in the end, whatever the initial plausibility of the claim, its truth will require the same degree of evidentiary strength.

Sometimes a very plausible claim with strong evidence, to the point that the claim is accepted as factual, can be overturned by additional weak evidence. The claim about the scale independence of the role of gravity was overturned by the evidence from mathematical research into the relationship between quantum and gravitational fields, which show that gravitation does not in fact extend to the atomic scale of matter. Stronger evidence was later found to confirm this counterintuitive truth about nature.

Another approach to the relationship of claims and evidence comes from the legal system, which can be applied to science in a general way. Testimony from a witness is considered evidence, and the strength of the evidence could depend on the characteristics of the witness. If a dozen highly respected members of the community, with no particular motivation to lie, all testify to something, and they are opposed by a single person with a criminal record and a strong reason to evade the truth, the weight of the evidence will clearly fall in one direction.

How does all of this relate to evidence for a Divine being, a Creator, God? It is clear that scientific proof for God’s existence does not exist. But what about evidence? There is evidence both for and against the existence of a supernatural Being, some of it coming from what we know scientifically about the natural world, since God’s creation should be expected to reflect something about the nature of the Creator. Most of this evidence relates to the proposition that there is something missing in a purely naturalistic model for how the physical and biological worlds came to be and how they work. The fine-tuning of so many physical and cosmological constants, the origin of life, the origin of biological information, and the mysteries of consciousness are some of these pieces of evidence. Calling them God of the gaps does nothing to dismiss them as evidence, since all evidence can at some future point be refuted by new discoveries.

A great deal of evidence is based on the absence of alternative theories (including the nature of proteins as the genetic molecule). But in addition to that kind of evidence, there is an overwhelming amount of nonscientific evidence for the reality of Jesus Christ as God incarnate. This includes historical and written evidence, eyewitness testimony, and subjective stories of the impact of religious belief on millions of people. One can easily dismiss the claims of human beings as false, illusory, impossible, etc., but again, those kinds of judgments can at most lower the strength of such evidence, they do not remove it from consideration. If they did, our entire legal system would collapse.

So it is completely false to claim that there is no evidence for God. There is both strong and weak evidence for God. As time goes by, some evidence will be dismissed, and new evidence will be discovered, as has happened in the past, in both science and philosophy. Meanwhile, each of us are free to believe in our own subjective evidence in salvation from grace and the deity of Jesus, without need to fear that all evidence for our beliefs is lacking. When the time comes, each of us who believe will learn that we were right, and those who do not believe may learn they were wrong. But if believers are wrong, we will never find out, and neither will nonbelievers learn they were right. Until then, follow all the evidence, weak and strong, and keep the faith.  

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How to Write a Scientific Paper

Most people not working in science have no idea of what it means to write, review, and publish a scientific paper. Why should they? Scientists learn the basic rules and customs from our mentors and advisors in grad school, and then continue learning by trial and rejection.

The overall style of a scientific paper is quite different from other written forms of communication and can be off-putting for casual readers. The generally forbidden passive voice is encouraged, so sentences like “In order to test this hypothesis, an experiment was designed….”. are perfectly common and acceptable. The great majority of papers are divided into well-defined sections: Introduction, Methods (sometimes called Materials and Methods), Results, Discussion, and References. Figures and Tables are distributed mostly in the Results section, each with legends that can be quite long and detailed.

Introductions are short summaries (a few paragraphs long) of what the paper is about, including some mention of work that came before, with lots of references. This means something like “Previous workers (Smith 2012, Jones et al. 2014) have found that standard evolutionary models do not fit the kinetic data…” There is no explanation of basic knowledge (like what is evolution or enzyme kinetics) since the reader is assumed to be a trained scientist in the field or a related field to the subject of the paper.

It is unheard of to make a new claim without any reference to previous work—even breakthrough revolutionary works of genius must refer to previous work in the area. There is also a practical reason to include lots of references. The odds are high that some of the people being referenced will be reviewers, and nothing makes a reviewer more cranky than not seeing his/her own work referenced. (Yes, I speak from experience.)

The Introduction is generally followed by a Methods section, which goes into varying amounts of depth and detail, depending on the field. When PCR was a new technique, I used to present all the PCR conditions and primer sequences. Now, people just say “by PCR”.

The Results section is required to be crisp, to the point, and limited to basics. No flowery language is allowed. A typical sentence might read “We found no evidence for homeostasis (Figure 1).” The heart of the Results section is the data, presented in figures and tables. Some Results sections can be incredibly dense, with a huge amount of information crammed into one sentence. Here is an example from a paper I recently read:

Figure 5 shows that a genotype’s vertex degree and its number of latent phenotypes are weakly, but significantly positively correlated (Spearman’s r = 0.13, p < 1.2 × 10−41), indicating that mutationally robust circuits have an increased capacity for exaptation.

Then comes the fun part, the Discussion. Here the authors are allowed a bit more leeway in terms of eloquence, and even some degree of deeper thought. Here, and not in the Results section, the meaning of the results can be discussed, almost always in the context of what everyone else has found, both in agreement and in contrast with the work presented. Thoroughness is key. Leaving out some key work by other groups is often fatal. All Discussions must include at least one paragraph of self-criticism, wherein the authors point out weaknesses of the paper, whether in methodology (“Our sample size was considerably smaller than that of Wheatly et al.,…”), or in the consistency of the data. All instances of disparity between the presented work and that of others should be brought out, and explanations for these disparities must at least be attempted. 

The entire approach is decidedly low key. A paper that purports to have “made a significant and groundbreaking discovery that will change the nature of how we think about…” would not even get sent out for review. It ain’t the internet. The use of qualifiers like “could” or “might explain” or “is consistent with” or “lends support to the idea that” are very common. Phrases like “we have proven that” simply do not appear (with the exception of mathematics, and some rare physics papers).

Books aren’t scientific papers, of course, so none of this applies to them. I felt a huge sense of freedom while writing my first trade book, since I realized I could say almost whatever I wanted to. (I still included lots of graphs, which turned out to be a mistake for sales, but that’s another discussion.)

Is this the best way for scientists to communicate? I don’t know. The style of 19th-century papers was completely different. They were long, and long-winded, with philosophical musings and off-topic tangents, all now forbidden. Some people have said we need to reform the way we write papers. Maybe, but I will bet it won’t happen, at least not any time soon.

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A Planck Era in Biology?

Laws of physics control most of how the universe operates. These laws are believed to have come into being very soon after the Big Bang—specifically, a Planck time (approximately 10^-43 seconds) after the Big Bang)—and it is generally agreed that we can know nothing about what happened before that moment.

In biology, we don’t have mathematical laws with the precision and certainty that we have in physics, but enough is known to be confident that biology is a natural science and is therefore governed by laws, even if they have not been elucidated to the same extent as has been done for the non-living world. Among those laws is the theory of evolution by natural selection, which is not yet complete, but it has passed all tests and remains the bedrock of biological theory.

When combined with modern knowledge of genetics, physiology, and cell biology, the theory of evolution helps to guide us in understanding the great majority of biological questions and previously unsolved mysteries of life.

As the universe, life has a history. Science can look back in time to before there were human beings, before there were primates, or mammals, or vertebrates, all the way to the time when the only living creatures on the planet were single cells. And although as we go further back, we become less sure of what we know, we do know that the basic principles of biological science, including biochemistry and evolution, still hold.

But like the Big Bang that started physical reality as we know it, there was a beginning to life as well, and it was at some point before the existence of the most primitive living cell we can imagine. We call this hypothetical creature LUCA, which stands for the Last Universal Common Ancestor, since such a cell contained all the components required for life, and from this cell all further life could evolve by the processes we understand.

We can postulate that LUCA emerged in some way from protolife, but up to now, we have no clear path to understand anything about that emergence. It is my contention that such understanding of the origin of life before LUCA is, analogous to the time before the Planck era, impossible.

To continue the analogy: before LUCA, the laws of biology as we know them today did not exist; in particular, I maintain that the mechanism of evolution by natural selection was impossible. Since there is general agreement that LUCA could not have appeared spontaneously from chemical components, and therefore it must have evolved, we are left with the conundrum that we must have an evolutionary process before such a process was possible.

The only alternative is to postulate an alternative evolutionary process that does not rely on selection or on accurate replication. There is no theory that allows for the evolution, meaning the gradual change over many generations of a population of cells, that does not require high accuracy in replication of the cellular phenotype from one generation to the next. If a cell is able to improve in any way (energy usage, metabolic efficiency, longer life, more mobility, better biochemical reactions, etc.), but that improvement dies when the cell does and is not inherited by the daughter cells, the improvement is simply lost. Consider the following mathematical statement of gain of fitness (F) from generation n-1 to generation n due to selective advantage (S):

Fn = S(Fn-1)

Without accurate replication, this equation fails, since there is no relationship between Fn and Fn-1. Fisher’s fundamental theorem of natural selection, postulating an increase in fitness with time, would not hold.

The eminent pioneer of evolutionary biology and abiogenesis Eugene Koonin published a paper entitled “The Biological Big Bang Model for the Major Transitions in Evolution” that explores similar ideas, except that Koonin proposes a way to fill some of the gaps in biological evolutionary theory, postulating several Big Bang-like events. Koonin uses the expansion model from cosmology but he does not apply his model to the origin of life, nor does he suggest an analogy to the Planck era in cosmology.

It is my belief that just as in the origin of the universe, the origin of life will require new paradigms (including, perhaps, those now considered to be outside the boundaries of naturalism) to be understood.

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Music Lesson

I studied chemistry in college and biochemistry in graduate school, and I became a professional scientist. I love science, and although retired, I still work at it (just without a lab). But science was not my first love or my first choice as a profession. That was music.

I went to the High School of Music and Art in New York City, where I played the flute. Not very well, unfortunately, and I soon understood that my love of music was not going to translate into a performing career. But I still always love listening to music (and I occasionally play a little guitar or recorder for myself).

During my first week at my high school, I noticed an odd sight in the cafeteria. A short, stubby, not very attractive guy was sitting eating his lunch surrounded by four or five beautiful girls. As he sat there, other girls came by and talked to him and smiled. Sometimes guys would approach him and wave or nod. This kid would nod back, but he didn’t appear to say much.

I noticed the same thing with the same kid a few more times, and I finally asked a friend who had been in the school for a year already why that ugly kid was so popular. He looked over at who I had indicated then stared at me. “Are you kidding? Don’t you know who that is?” I didn’t. “That’s Jerry G.” I was still at a loss, and I confessed I had no idea who Jerry G was, or why that was an answer to my question. My friend told me to show up at one of the after-school jam sessions that some of the better student musicians held on Fridays.

When I did, I saw a bunch of mostly seniors and juniors with a variety of instruments, and there was Jerry holding a trumpet. He was sitting on a chair a bit apart from the small group of brass players who were jamming together on a jazz piece. But then they stopped, and Jerry stood up. Five seconds after he started playing, I felt like I had been knocked out of my seat and pulled up to the ceiling and then dropped down again. I had never heard anyone before (nor since) play the trumpet that way. Clear, powerful, brilliant. When his solo was over, and I could breathe again, I understood everything. Jerry didn’t need to be good looking, clever or funny. He didn’t need anything other than what he had – an enormous talent.

Jerry did not become a famous trumpeter – I never heard anything about him after we graduated. But whatever transpired in his life, I know that his talent must have been there for him whenever he needed it.

I might mention another person I met at Music and Art, a beautiful shy quiet girl, with an amazing voice. I remember a party at which I heard her sing, and I fell in love (not a rare occurrence for me). We spoke a few times, and I had the sense that she was a kind soul, but was way above my level in both music and spirit. Her name was Laura Nigro, and we pronounced her last name as Nygro rather than Neegro. When she became a famous song writer/singer she changed it to Laura Nyro. If you dont know who she is, listen to her on YouTube, and you will understand my gratitude at having known her, if only briefly.

At that time, I also had a friend who was a first-class drummer, and who had spent some time taking lessons at Julliard. He invited me to go with him to hear a recital of Julliard students, and I went. I was disappointed when we entered the hall, since the program specified that the day’s recital was going to feature string players, and I was always bored by violinists (being a wind chauvinist).

I sat through a number of very good and very boring performances by a wide variety of students from all over the world, who played extremely well, but still, it was always the violin. I was slumping in my seat, almost asleep, when my friend nudged me. “This could be interesting,” he said. I looked up and saw a student about my age struggling across the stage on a pair of crutches. “Wait,” I said. “How can he possibly play? He needs to hold his crutches.” The kid got to the front of the stage, sort of half sat on a tall stool, and brought up his violin, which he had been carrying under one arm. And he began to play. I sat up straight. It was the second time in two years I had heard a young genius play music. Again, the musician was flawless, and the music was powerful and sublime. I was transported. My friend commented that maybe he was compensating for being a cripple, which was a word people used back then. We agreed that it was an astonishing performance. I remember looking at the program to see who this kid was, but it was a foreign name that I couldn’t remember the next day.

If you know much about modern music, you will have already guessed the truth. Yes, I was one of the first people in this country to hear a performance by Itzak Perlman, generally considered to be the greatest living violinist, and some think the greatest ever.

So why have I told these 2 stories about music in this blog about science and faith? Because I found these experiences uplifting. God has endowed all of us with gifts, and first appearances (being funny looking or disabled) are useless in discerning the endowments of another human being. I have in my career met numerous similar examples of shining talents in science, housed in broken or unattractive receptacles. We all have seen this for all kinds of talents, including preaching the word of God, or writing amazing sermons. And what about those of us who are simply mediocre at most things, with no outstanding abilities like Jerry or Perlman? I maintain this is impossible, and that all human beings have been endowed by the Creator with many gifts, even if they are not at all outwardly apparent and cannot be seen in any kind of  performance. Even me.

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