Here is the link to my recent talk at the American Scientific Affiliation Washington DC Metro Chapter, on June 24, 2016. Its a bit dark, and its long, but about half of the video is discussion from the audience, which is worth hearing.
Among the voices in the Discussion (the camera didnt move, so you cant see them) are Mike Beidler, Keith Furman, Anna Rich, Tom Burnett, Paul Arveson, Langston McKee, and a number of guests whose names I didnt write down.
Genes are amazing things. They are storehouses of information. They are also able to copy themselves (with some help), and they are the reason I am here typing. In the 1970s, evolutionary biologist Richard Dawkins had an insight that propelled him to write a book called The Selfish Gene. It was a brilliant, carefully thought-out theoretical and philosophical breakthrough in biology. It was also badly misunderstood. In the years and decades that followed publication, people who had not actually read the whole book complained that genes are not really selfish, since they have no minds to entertain such notions, and anyway, the term selfish is a negative one, and it makes evolution seem like an evil doctrine (which creationists already agreed it was).
The book makes it quite clear that our concept of selfishness has nothing to do with the point. What Dawkins is saying is that genes are the key components of the evolutionary process that involves selection of the most fit varieties of life. And since genes are the ultimate controllers and determinants of all the characteristics of all living organisms, what we end up with are genes that create the best possible cellular structures and features to allow those genes to keep on existing.
In other words, the selfish gene concept was actually a distilled and targeted demonstration of the root mechanism of evolution – natural selection. This is possible because genes do two things extremely well, and these happen to be the two most important things in biology: they replicate themselves with a very high degree of accuracy, and they code for all of the phenotypic characteristics of the cell that are the target of natural selection.
Think of a school board that is trying to decide between two textbooks. They do an experiment in which one class of students uses one text, and another class uses the other text. The students who used the first book do better on an exam than did those who used the second. So the School Board decides to order more of book 1. The books are the genes, the students’ knowledge are the phenotypes, the exam is the environment, and the school board is natural selection. Textbook 1 (which the school board didn’t even read) survives and becomes the only book in use. Nothing selects the genes themselves, but when the information in the genes is translated into the phenotype of the cell, the selection of the better phenotype leads to the selection of the better gene.
Dawkins’ view is that while the bird with the better eyesight might be better adapted and outcompete its rivals, what is successful is really the gene in that bird that coded for the better protein that produced the better eyesight. The phenotype (including later, the extended phenotype) is only a means to the gene’s ability to survive and continue to prosper.
It really is a very nice, consistent, logical and convincing idea. It’s also probably wrong.
At least that is the conclusion I have recently come to. I have always been pretty much a gene-centric kind of guy. As I said in my last post, I took the side of the replicator-first faction in origin-of-life discussions. I worked with genes and DNA, and I loved the way all of biology seemed to make good scientific sense if one simply ignored all the rest of life and just focused on genes. But alas, I can no longer support that view.
Part of the reason I am undergoing a conversion to a non-gene-centric view is the kind of new data and concepts about the extended evolutionary synthesis that I have discussed here before. Another part is that the idea of the gene as the absolute master of all of biology is just too simple, and biology is never, ever simple. The resurgence of the Lamarckian heresy; the importance of epigenetic effects, which can even be inherited (more heresy); and all of the results on niche construction, genomic engineering, and, of course, gene expression, have exerted their influence on my thinking.
I am not comfortable with all of this non-genic stuff. It makes everything more complicated and a lot harder. But if it is actually true that there is more to life than genes, I suppose there is no avoiding this. I have more to say about the whole subject, and I will in a later post. Meanwhile, it might be time to retire that well-known phrase “He has to do it that way. It’s in his DNA”. The big question now is, what do we replace it with?
Well, they aren’t brothers – they just share the same last name. I don’t think they knew each other. I don’t even know if they even knew the other existed. One of them, James is alive and well; sadly the other, Robert, died a few years ago. But in addition to their last name, they have something else in common. Both were scientists who changed my mind about evolution.
Bob Shapiro was a friend and a colleague of mine at NYU, where he was a Professor of Chemistry. For two semesters we co-taught a course in the School of Journalism on science for journalists. Bob was older than me, and senior in rank and reputation. We worked in similar areas related to the interactions of chemical carcinogens with cells and biomolecules. But Bob had started to become famous for something quite different -the science of the origin of life.
After teaching (we each lectured for about a half hour), we would go to a coffee shop in the Village near the campus and talk about science and life. At that time, I had no interest in Bob’s passion for the origin of life, but I was willing to listen to anything he had to say. With his quiet insistence he told me about his ideas and the state of the controversy that has always been at the heart of all scientific theories about the origin of life.
Life as we know it depends on two overarching characteristics: metabolism, which is the sum of all the chemical reactions that go on in cells, and genetic replication and expression, wherein the information that controls all of those reactions is copied and translated. Not surprisingly, the central controversy in the origin of life is about which of these two systems arose first. The replicator-first crowd will tell you (Richard Dawkins is the leading proponent) that replicating genes made of nucleic acids are the key and original components of living cells, and metabolism is a later invention, developed mostly to aid in the preservation and maintenance of the genes. The metabolism-first faction counters that nucleic acids need enzymes and other metabolic reactions in order to replicate, and life began as more or less automatic hypercycles of chemicals.
Bob Shapiro was one of the most convincing and outspoken advocates of the metabolism-first scenario. He published articles and spoke against the possibility that either DNA or RNA could have possibly been formed before life existed. I did not agree. I loved genes and DNA and was working on many aspects of genetics at that time (and later). I strongly admired Dawkins, and I was firmly in the replicator-first camp. But I didn’t argue with Bob; I cherished my time with him, and tried to learn as much as I could. Once the course ended, we saw each other rarely, working on different campuses and in different fields as he devoted more and more time and effort to his “hobby” of the origin of life.
I have not met James Shapiro, and had never heard his name until a few years back, when a friend suggested I look at some of his papers to gain an understanding of some new and interesting trends in evolutionary biology that is called the Extended Evolutionary Synthesis (EES). (That friend, btw, is an occasional commenter on this blog). Reading James Shapiro’s papers was an eye-opener for me. Like Bob, James is not a passionate fan of genes as the masters of all creation. In fact, James Shapiro is one of the leading architects of the EES, which is trying to replace neo-Darwinism as the standard model for evolutionary theory. According to James Shapiro, genes and their cellular and extracellular environments are engaged in a two-way interaction, with each having strong effects on the other. James calls this natural genetic engineering, and believes that a great deal of evolution that could not be easily explained by the traditional neo-Darwinian paradigm of gradual change from random mutations can in fact be due to rapid and dramatic changes brought on by the re-engineering of the genome by things like transposons, horizontal gene transfers, and large-scale amplifications.
I agree with James Shapiro. I have written about the EES in this blog and elsewhere (see “New Ideas in Evolutionary Biology, Parts 1 to 3, from August 2015), and am now working on some aspects of it. And I have recently decided that I also agree with my departed, dear friend, Robert Shapiro, that genes are not the be-all and end-all of life (although I still think genes are fantastic!). I have even come to the understanding that genes are not even essential for life (although they probably are for evolution. More on this later).
So thank you, Dr. Shapiro and Dr. Shapiro for your wise instruction, and may one of you continue to prosper and teach us, and may the other rest in well-deserved peace.
More on the subject of genes and their importance is coming. Watch this space.
Several decades ago, I welcomed a new graduate student to my lab. She had just graduated summa cum laude from a major Ivy League college, and she was as smart as can be. I put her to work on a project with happy anticipation of seeing wonderful results. I told her all about the project, which was to confirm a theory I had that the expression of two genes were linked in way to produce a specific phenotypic outcome. She spent several weeks learning the techniques and quickly mastered them. My technician, who was working with her, told me she was a quick learner, and her lab skills were great.
And then, I heard nothing from her. I asked her how things were going, and she just shrugged. My technician told me she was still working, repeating some experiments over and over, and she seemed depressed. One day I asked her to see me and tell me her progress. She came to my office reluctantly. After I asked her a few questions, she burst into tears. “What is it?” I asked her. “It didn’t work,” she told me. “I can’t get it to work”. This seemed strange to me. One of the secrets of scientific research is that most lab work doesn’t work. Not the first time. But her experiments were using techniques that we had mastered long ago, and based on what I had heard and seen, it didn’t seem likely that she had forgotten to add a crucial reagent, or had made a pipetting error, or set the temperature too high, or anything like that.
So for the next two days, I went over everything she had done in detail. It looked like all the experiments had gone just fine, and the results were clear But not at all what I had been hoping for. There was no correlation between the expression of the two genes and the phenotype. In other words, she felt she had failed because she had gotten the “wrong” answer.
I understood the problem. My student had only just finished a long, highly successful career of learning a gigantic quantity of facts and ideas, and she knew the right answers to any question one might ask her. What she didn’t understand was that when we do research, the right answer is anything that we find out, not what the Professor thinks the right answer should be. I tried to explain this to her, and she seemed to understand, and kept working. Pretty soon, she had found out why the original idea was wrong, and what the real mechanism was to explain the phenotype. I was thrilled, and we published several papers on the subject. But despite this success (and having her name on some pretty good papers), she never really recovered from her disappointment, and eventually left my lab.
I have always said that our educational system is not geared at all to the research enterprise. First, students are taught nothing about failure, which is the most common experience of all researchers. Failure is not a bad thing – it’s an opportunity to learn. When things go wrong, there is a reason. Usually the reason is just that somebody goofed, or the water wasn’t pure enough or something mysterious happened. And sometimes the failure is actually a hidden success waiting to be found.
Once, a postdoctoral fellow in my lab showed me a photo of DNA bands with one of the spots in the completely wrong place. We chalked it up to some kind of experimental mistake. But then we found it again, and realized that this was actually a new discovery – we had found a brand new allele of an important gene, never seen before.
I was reminded of this two weeks ago when I met Professor Stuart Firestein of Columbia University at a workshop I had organized. Firestein has a TED talk that I highly recommend, (https://www.youtube.com/watch?v=nq0_zGzSc8g) and has written popular books on the subjects of ignorance and failure in science. He got the idea for the books and talk from a course he developed and taught called “ignorance”. He had scientists come in and lecture on what was not known in their fields.
In addition to the problem that ignorance and failure are not properly treated in our educational systems, there is, I believe, a profound philosophical and perhaps theological aspect to the subject of ignorance in the sciences. This relates to a deceptively simple question – How much can we know? More about that in a future post.
My busy two weeks of meetings and deadlines is now past, and I can devote myself to important stuff like lying on the hammock, watching the garden grow, and blogging.
I recently started using Twitter to expand my social network life. I generally tweet a link whenever I put up a new post here or publish something. But more recently I have begun just tweeting stuff that I think of. Doing this in 140 characters is a challenge for me (as my regular readers can imagine), but I have managed a few times.
I don’t have many followers as yet (still learning the system), but a couple of recent tweets did get some attention. This was one.
If we knew ALL that happened through purely natural means, wouldn’t God be “redundant” (Dawkins)?
Nope, because “purely natural means” are the methods by which God creates. Without God there is no nature. This idea removes any force from the well-worn atheist argument that science can explain the world better than religion can. Of course its true that science explains how things work What many atheists cannot seem to fathom is that religion’s purpose is not to explain the world, but to understand the divine in human beings, and God’s purposes for us.
Atheists keep telling us that our “claim” that God exists requires extraordinary evidence. Why? We are not claiming to prove that God exists. Instead we witness to our belief in God. To the question, “what evidence do you have for the existence of God?”, there are several equally valid answers, among which is “none”. Other answers can range from purely subjective emotional experience (which are generally dismissed as psychological ephemera) to metaphysical views about the universe, which are generally dismissed as God of the Gaps, soon to be overturned by science.
The truth is that science “explains” nothing, it isn’t supposed to. What it does do is illuminate the laws and mechanisms by which things work, and events happen. It doesn’t tell us why things happen that way, or how they should happen, or what’s behind it all. Likewise, religion isn’t supposed to elucidate physical or natural mechanisms. When it used to do that, it was only because religion was the only organized thought system around at the time, so people turned to it for explanations.
The other tweet that garnered some interest in the form of retweets and likes is related to the same discussion on my views of how science and faith are related.
Science discovers and describes natural laws. Natural laws come from God. So how could science displace God? Science is distilled doxology.
I like that last 4 word sentence, and I thought it was worth reposting here.
I will not be posting here for the next week or so, since I am in the middle of a time crunch, with deadlines and obligations bearing down from several directions. I hope to get back to speed after I return from the Annual United Methodist Conference for the Washington Baltimore District, June 1 to 4th. (I am the Lay member of the conference for my church).
Blessings to all, and peace.
I have studied many things in my long career in biological research. Most of my work was on applied biology. I worked, published papers, and got grants in environmental health sciences, toxicology, cancer research, molecular epidemiology, population genetics, gene-environment interactions, genetic susceptibility, metabolic gene polymorphisms, and others. I achieved a brief and modest degree of recognition in the field of molecular carcinogenesis in the early 1990s, and again in the field of human genetic susceptibility to environmental disease in the 2000s.
But during this entire 40-year career in research (this year marks the 40th anniversary of my Ph.D. in Biochemistry), I was always most interested in something quite different: theoretical biology.
I was told by a senior researcher once that theoretical biology is an oxymoron. Biologists don’t do theory. There is a Journal of Theoretical Biology, in which I have published a few articles, but the journal has always had a low citation index (it’s now about 2, but used to be below 1), and my papers there are among the least cited of any of my papers.
My favorite paper, the one I think is the best paper I ever published, is called
Fractal Properties of the Human Genome. J. Theor. Biol. 230:251-260, 2004. This paper has been cited 20 times, which isn’t bad, but not great for a 12-year old paper. The first two or three years after it was published, it got no citations at all. I published 7 research papers in 2004, with an average citation count of 48. The fractal paper has the lowest number of citations in the group for that year.
I have blogged on this topic before (see Biology, the Lawless Science). Of course it isn’t news that biologists don’t like theory, nor that they don’t understand the value of theory. And theoretical biology is hard. Many papers in the field are from mathematicians who want to apply their favorite models to biological issues, and their papers are not accessible to ordinary, non-mathematically minded mortals.
But the good news, at least for me, is that some of this anti-theoretical bias in biology might be starting to change. There are some fields, like evolutionary biology, where new models and new theories are emerging, although nothing like a universal law has yet been brought forth.
I have mentioned my own work when I started this blog. I thought it would be a good idea to try to derive some basic laws or principles for the way that gene regulatory networks (GRNs) operate. GRNs have become recognized as potentially key features of evolutionary progress. Such networks can be represented by mathematical arrays or matrices of gene interactions, and should therefore be highly susceptible to theoretical analysis. And many scientists have been working in this area. Andreas Wagner, whose book The Arrival of the Fittest made a big splash in the modern field of extending the evolutionary synthesis beyond neo-Darwinism, bases much of his argument on his findings of how robust regulatory networks can lead to innovations in evolution.
I have also made some modest findings in this field on a simpler level, but they are interesting and I am writing them up for publication in the scientific literature. If and when these papers are accepted I will post some of that work here.
Throughout my career, I have published a lot of findings, results, even some ideas and concepts. But I would be really thrilled to be able to find some kind of fundamental law that can explain any aspect of that marvelous, astounding and absolutely unique thing we call life. We’ll see.
It has become quite popular to doubt the reality of free will. The famous atheist Sam Harris has a book about this, and the claim that free will is nothing more than an illusion can be found throughout modern atheist screeds. The idea is that we don’t have free will, because everything that happens is a direct or indirect consequence of a long chain of previous causes (strong determinism). We cannot possibly be aware of all of these causes – some are subtle and don’t reach our conscious minds; others are simply beyond our knowledge. According to this view, even though it doesn’t “feel” that way, my decision to write this post was not actually due to my free will, but to an enormous variety of pre-existing conditions and events that inevitably led to me sitting here and typing away.
Aside from the fact that such an idea is far from provable (despite the absurd data that Harris presents about the timing of actions vs. thoughts, which are not even relevant to the issue), there is another problem with this concept. It is in direct contradiction to another very important premise of modern atheism.
This is the atheistic idea that biological evolution is undirected, purposeless, and totally accidental. Gould put it into words by saying that if we started from the beginning and played the tape of evolution again, we would get totally different results and probably no humans. So you can see the problem. If there is no free will, because everything is pre-ordained from the beginning, or from any point in the history of the universe, then why is evolution not included as something that could only have taken the path that it did? Is evolution actually capable of free will, but humans are not? Or is evolution a result of the power of accident to overcome previously existing conditions – but, for some reason, active decision making does not have the same power? How can there even be such a thing as an “accident” anyway, in a purely deterministic universe?
In other words, if free will cannot exist, then the tape of evolution would have to play exactly the same way, including me typing these exact same words, the second (or billionth) time around. So one of these contradictory ideas is clearly wrong. Which one?
I think the answer is both of them. Free will clearly exists, and many animals have it as well as people. And while evolution is somewhat dependent on accident, we now know that the idea that “anything goes in evolution” is false. The number of constraints and examples of convergence that have been seen on both the organismal structural level and the molecular biological level tell us that if we replayed the tape, we would get something pretty close to what we have. I might be a bit shorter than I am, and maybe a bit smarter (the same for you, of course), and maybe there wouldn’t be any horses, but otherwise, some kind of animal looking a lot like me would be doing something pretty similar to typing words on a screen – and doing it with 10 fingers, in fact.
Wouldn’t it be nice if the folks who think that all religious people are illogical, irrational, uneducated fools actually spent a bit more time thinking logically themselves? Well, I suppose it isn’t their fault – after all, they have to think the way they do. They have no choice about it, right?
Note: For an earlier discussion on free will and atheism and science see this post
I grew up in the middle of Brooklyn, NY, so I missed out on the whole trees and flowers thing until much later. But there were some advantages to being in NY. My parents brought me to see quite a few plays, shows and films – mostly those for kids, but some others as well. Among them, I got to see the live Broadway version of West Side Story, which made a huge impression on my pre-adolescent heart and soul.
Just last week, I went to hear my stepson’s high school band concert, which included a couple of songs from the show – “Tonight” and “Maria”. Beautiful songs, but neither is my favorite. That would be the song that is sung twice, and that in the film version dominated the ending of the story – “Somewhere”. The story of Tony and Maria ended tragically. And when I first saw the show, in 1959, it could only have ended that way. And yet, that song has lyrics that promise hope for the future, hope for a time and a place that seemed impossible back then.
There’s a place for us,
A time and place for us.
Hold my hand and we’re halfway there.
Hold my hand and I’ll take you there
Somehow,
Someday,
Somewhere!
That “someday” has arrived. And the somewhere is here, and it is most places. People can marry the person they love, whether they are the same race or ethnicity or not. It is no longer, as it once was, a scandal or an outrage or even illegal. If the composer of West Side Story had known that “Someday” gay people could get married, he would have been incredulous and joyful.
The world today (as President Obama just said at Howard University) is better than it was. Yes, we might only still be halfway there, but we are moving in the right direction. Trump and his followers? The last-ditch resistance to the acceptance of love as the wonderful unifying force that changes the world
When Jesus came to us, he preached this. He told us that the Kingdom of God is at hand, that we are not stuck in an unchanging static world, that we can make it better, that it should be better, that it will be better. He told us, all of us, sinners, the poor, the rejected, the despised, that there is a place for us, a place in Heaven and a place on Earth, maybe not in the present, but in the future, and that prophesy has come true. He told us “Hold my hand, and I’ll take you there”, and so many of us have done that and have seen the glory of God’s love.
Yes, there is progress. This world, this reality we know and study, is full of progress, and always has been. We humans have progressed in my lifetime, and throughout history. And for those who deny that evolution has a progressive direction, like the late great Stephen J. Gould, I can only say, please look at the evidence. I know that most living creatures are still bacteria – that is not the point. At one time there were no organisms made of more than one cell, and now there are. At one time, there were no creatures with brains, and now there are. At one time there were no birds, rabbits, lions, or cuddly cats and faithful dogs, and now there are. And at one time there were no people, nothing that could write blog posts, or read or cry or laugh or tell stories. Now there are. Some deny that this is progress. But I know that it is.
We aren’t there yet; we don’t even know what “there” is. But what matters is that we are moving in the right direction. Tony and Maria today are married, and watching their oldest child graduate college. Seated around them, other parents are crying and applauding, and they are all the colors of humanity, all mixed together, celebrating the wonderful onward march of their families toward that better Somewhere and Someday that await us all.
Parsimony has become very popular with scientists and philosophers. The idea is that the simplest explanation for any phenomenon – the one that includes the fewest possible number of causal factors – is the best explanation. This principle was used by William of Occam in logical arguments and has been popularly called Occam’s Razor. It is often applied to situations where one must choose between alternate theories, one of which includes a fewer number of causative factors or a simpler mechanism than the other.
“Entities must not be multiplied beyond necessity.”
“We are to admit no more causes of natural things than such as are both true and sufficient to explain their appearances.”
“…the simplest hypothesis proposed as an explanation of phenomena is more likely to be the true one than is any other available hypothesis, that its predictions are more likely to be true than those of any other available hypothesis, and that it is an ultimate a priori epistemic principle that simplicity is evidence for truth.”
The idea certainly seems reasonable, but is it correct? It might be for most physical theories, but it’s quite wrong when applied to biology. There are in fact no simple phenomena in biology, and simple hypotheses simply fail on a regular basis. Biology works according to its own principles and laws, which are not the same as the logical constructions of the human mind. Nor are these laws easily reduced to the laws of physics. Simplicity might be evidence for truth in physics; it almost never is in biology. Here are a couple of examples:
Which hypothesis is more likely to be true?
Note that 1 is sufficient to regulate the amount of A and B. It is the simplest solution. But it is almost never what actually happens. The correct answer is usually 4. One example is the control of the synthesis of deoxyribose trinucleotides (used in DNA replication).
Here is another one. We know that coloration in plants and animals is usually of some evolutionary benefit or purpose. Which hypothesis is likely to be true for fish living in the deepest ocean where no light exists?
Yes, the second one is correct. Fish living in the deepest part of the ocean have amazing colors – brilliant yellow, blue and orange patches on their scales that are never seen since all the fish and other creatures in this environment are blind. The fish have such amazing colors because in that environment, colors are irrelevant and cannot be harmful (by attracting predators, for example). They are the result of random mutations in pigment genes (carried over from their ancestors) that produce a phenotype with no detrimental effect on the survival of the individual, and are therefore never selected against.
Welcome to Biology.
There is a popular belief that phenomena have a single, simple explanation, and that once the best cause of anything is identified, all other potential causes can be ruled out. Like the principle of parsimony that underlies Occam’s razor and the other quotes above, this certainly does not work in biology. Whether at the organismal level or at the level of biochemistry, many different causes can produce the same effect. And one cause can produce a myriad of effects. This is why biological reality is so complex and so hard to capture in mathematical terms. It is true for metabolic pathways, for gene regulation, for animal behavior and for evolutionary biology.
In the next post I will discuss the implications of the failure of parsimony and simplicity in biology for theology. Comments from readers who might have a view on this issue are especially welcome here.
 | Bruce Cooper on An Announcement |
 | SheilaDeeth on An Announcement |
 | dgilmanjm on Enemies |
 | Lightness Traveling on Enemies |
 | Arnold on Enemies |
The Book of Works 