The Book of Works

Another rather interesting trait of slime molds and related organisms is that they are capable of rather impressive feats traditionally thought to be limited to “higher” animals. These include behaviors like problem-solving skills and the ability to learn. Amazingly, they also display the ability to anticipate environmental changes based on prior experience. Still, just like bacteria, the amoeba-like cells in slime molds do not possess an actual animal-like nervous system. If we think about it, from our admittedly biased perspective, the absence of a nervous system makes the behavioral repertoire of bacteria and slime molds even more astonishing.
Oné Pagán: The First Brain: The Neuroscience of Planarians (2014),

I looked up at the sky and all around and saw no sign of any birds. I was standing on a rocky beach in Maine. I had a bucket of lobster shells, which I threw onto the beach. A minute later two seagulls arrived from somewhere and began to feed. I knew this would happen (I had been disposing of lobster remains this way for many years), and I knew that the long-distance visual capability of seagulls was remarkable.

So is the vision of hawks, the strength of spider webs, the speed of deer, the cunning of squirrels, and so on. I know that all these features and every other characteristic of  living creatures are the product of evolution by natural selection. But I can understand why some people see the hand of an intelligent designer in the amazing structures and function of flowers, bees, and all of life.

And I now believe they are right. I think there is in fact an intelligent designer at work that explains all the magnificent beauty of biological life. But when I use the word intelligence, I mean something different than the kind of intelligence we are most familiar with.

We solve problems with our intelligent brains, as do many other animals. But is brain-centered intelligence the only form of intelligence that can exist? Apparently not, since we already know the brilliant things that computers and automated machines can do. We might be able to imagine other forms of intelligence that have nothing to do with the complex neural electrical circuits that are the components of smart brains.

Actually, all living creatures, including single-cell organisms like bacteria, possess a form of intelligence that is not remotely conscious or like anything based on brain function. The dictionary definition of intelligence is the capacity for learning, reasoning, and understanding. Clearly a single bacterium, or even a single ant, is unlikely to exhibit any degree of reasoning or understanding. But populations of bacteria and other “primitive” creatures do show the capacity to learn, and, depending on how one defines the words, to reason and understand. When observing these organisms, we are tempted to describe their behavior in anthropomorphic terms, because they seem to resemble familiar human characteristics.

For example, the quote by my friend, Dr. Pagán illustrates the remarkable way that slime molds can behave. Thousands of individual M. Xanthus bacterial cells can coordinate their behavior in order to more effectively attack and degrade other bacteria.  Many bacteria living in soil, with restricted mobility, solve the challenge of migration by growing in a pattern that results in net migration in a particular direction. Some single-cell amoebae are able to construct shells of glass from sand grains. The idea of a single cell building its own shell is remarkable.

The intelligence of “lower” creatures is not related to neural electrical impulses – it uses a completely different platform. What we see in all living creatures, no matter how simple and small, is biochemical intelligence. Bacteria, amoebae, ants, and plants communicate and perceive through chemical signals, not electromagnetic ones.

Bacteria use biochemical signals and receptors for those signals to communicate to those around them that they are there, and when a critical mass appears, the community of bacteria take the appropriate action (produce light, or virulence, etc.). Plants of all kinds also use biochemical signaling both for internal and external communications. No tree, flower, or grass possesses any neural systems.

Even in advanced, large creatures like us, most of the cells in the body act on signals from neighbors and hormones. The great majority of the activity of liver, skin, intestinal mucosa, and other somatic cells is invisible to the brain, and the very existence of a large intelligent brain is irrelevant to most somatic cells.

Biochemical communication between cells, the foundation of intrinsic biochemical intelligence, depends on the production of very specific proteins, which can act as signals and receptors, as well as on enzymes involved in the synthesis and degradation of these signals. Like all proteins, those involved with communication are produced in the ribosome according to the program of the DNA sequence and the genetic code. The genome determines not only what signals are produced and what the receptors do in response to binding to a signal, it also determines when this happens, thanks to intricately complex gene regulatory networks.

The actions of the signaling proteins and their receptors are automatic and preprogrammed. The organism has no choice in what happens when a signal is bound to a receptor and the bound receptor initiates some action by the cell. This might call into question whether we should really consider this to be intelligence, any more than we deem a computer intelligent.

But, in fact, there is more to IBI than chemically predetermined actions following the receipt of a chemical signal. When it comes to animal intelligence, we consider interaction with the outside world as an important part of intelligent decision-making and the exercise of will. Animals interact with the environment by means of their senses, and feedback from sensory stimuli is an essential part of neurological intelligence. Such feedback tends to be swift and in real time. A fox smells a rabbit, approaches slowly, sees the rabbit, and decides to give chase. The sensory input leads to the intelligent decision to pursue the prey.

Cells also have a way to get feedback from their environment that allows for intelligent choices and decision-making, but it is vastly different from animal sensory perceptions. The way bacteria and other simple organisms get the feedback they need is by dying.

Put another way, the feedback that tells cells whether their communication, defense, and other systems important to their lives are working well or need to be improved is natural selection. The best way to see this in action is the “viral” video from Harvard that shows bacteria evolving and expanding into zones of increasing concentrations of poison. As the bacteria spread, most of them die, and the survivors have undergone mutations allowing them to thrive in higher poison concentrations. It is this same process of evolution by natural selection (environmental feedback) that allows for the origin of the protein signals and receptors and is responsible for their continuous improvement and adaption to changing environments. The feedback here is extremely slow compared to sensory feedback, but it has the same effect. Remember, it isn’t the individual bacterium or social insect that counts, but the whole population.

This means that the intelligent designer is actually every biological population of organisms, and the method of design is populations using their intrinsic biochemical processes of communication and protein synthesis, coupled with input from the outside world by means of natural selection to give feedback regarding what works and what doesn’t. This is design by intrinsic biological intelligence.

When I first heard about epigenetics, I hated it. I still do, in fact, but I am slowly beginning to accept the fact that epigenetics is a fact. And it’s a terrible fact, like all facts that force one to radically change one’s long-held ideas.

In the 19^th century everyone knew about inheritance, but nobody knew about genes. Two similar theories of evolution were proposed, one in 1809 by Lamarck, and 50 years later a more complete one by Darwin. Both men proposed that species can change their characteristics over time and that such changes can even produce new species, and both saw the role of the environment as critical to this process. Lamarck’s theory was that when creatures experienced environmental changes to their characteristics, these changes could be inherited, resulting in evolution of the population.

Darwin’s theory saw evolution proceeding in two major steps. First there were heritable changes, and then environmental conditions selected which organisms would survive and reproduce based on the phenotypes produced by these inherited changes.

The 20^th century saw the flowering of Mendelian inheritance into a major science. The concept of the gene – the hypothetical inheritance particle – was substantiated by the discovery of the structure and function of DNA. Darwin’s theory was confirmed, Lamarckian ideas were utterly rejected – both on theoretical and observational grounds – and neo-Darwinism was born.

And that’s how things have stood for the past 60 years or so. The inheritance of acquired characteristics, as Lamarkian evolution has been summarized, was dismissed as nonsense, with no evidence and lots of counterevidence.

Until recently. Don’t you love science? It’s never boring. I first heard about epigenetics when I was researching the environmental causes of cancer. The idea was that in some circumstances, certain parts of the DNA molecule are modified with methyl groups that change the expression (usually by repression) of a gene. This modification of gene function can act like a mutation, since if a gene is not expressed, it’s just as if it had undergone a mutation. By itself, these findings were not terribly dramatic, because such methylation and its effects could not possibly be inherited, so I (and everyone else) thought of these epigenetic changes (called marks) as having no impact on basic Darwinian theory.

Oops. Over the past decade, it has become clear that sometimes these epigenetic changes, due to various exposures or environmental influences, can in fact be inherited, even after the exposure is over. At first it seemed that this only happened for a few generations. But no. That would be too easy. It now appears pretty likely that some epigenetic effects are long-lasting, perhaps permanent, just like a mutation in the DNA sequence. The crucial difference is that mutations are very rare, accumulate slowly, and are random, while epigenetic effects can be very rapid, much more frequent, and targeted to specific genes.

Welcome back, M. Lamarck. Having been educated for over four decades that Lamarckian evolution is a nonsensical, utterly wrong idea, I was not happy. But that’s science. Physicists have gone through this sort of thing routinely in the past century or so, and now it’s the turn of biologists.

The implications of long-term inheritance of epigenetic alteration of genomes are staggering. If epigenetics is a real mechanism of evolution, as real as the neo-Darwinian mechanism of mutation and natural selection, then everything in biology changes. The good news is that a lot of tough question might be answered, such as how phenotypic innovations can lead to major and rapid appearance of new biological features, without needing the very slow, laborious process of mutation accumulation (allelic variation) followed by selection. The bad news is that almost everything we thought we knew about evolution must now be re-thought.

As in all such paradigm shifts, traditional Darwinian genetic evolution is not disproven; it has been modified to include a host of new mechanisms (epigenetics being a major example, but not the only one). Lamarck is back, with his own molecular mechanism of epigenetics to be joined with Darwin’s genetic mechanism. The theoretical and predictive implications of this merger are both incredibly complex and very exciting. I propose that the new theory of evolution combining inherited germline mutations and inherited epigenetic marks be called Darmarckian evolution. And to all my colleagues who share my horror at such a heretical vision of how biology actually works, I can only say (as I have had to say to myself), “It’s science – deal with it”.

The first issue of the online magazine, God and Nature with yours truly as Editor-in-Chief has been released at this LINK.

The focus topic is “Chance and Design” and it also includes an essay by me (sent in and approved before I became the chief). It did of course, take a lot of work to put it all together, but not as much as I feared. The hardest part of it was wrestling with the Weebly software (I much prefer you, WordPress, but I inherited the Weebly). Anyway, now I can take a brief vacation until I start promoting and editing the next issue, due to come out in July.

I encourage readers of this blog to think about submitting something. Take a look at the “Author Guidelines” for more information on what we’re looking for. The ezine is put out under the aegis of the American Scientific Affiliation (ASA), and it would be good for any writer wanting to publish in G&N to join, but not required.

Anyway, I hope you get a chance to read whatever interests you, and would love your feedback, including suggestions for improvement etc.

The hare, having lost the most famous race in history, eventually gathered up his dignity and asked for a rematch. “This time I’ll be careful” he told himself. “I wont be overconfident, I wont get distracted, I wont let my urges and instincts get in the way of success. I will redeem myself and the reputation of all hares, not to mention rodents and mammals in general” As we can see, the hare had not completely shed his feelings of self importance. But he trained hard, not so much for speed and stamina, because he was smart enough to understand that these were not his problems, but for concentration, will power and discipline.

On the day of the race he showed up at the starting line a half hour early, to find the tortoise taking a nap in the shade. A number of animals serving as judges, as well as a large quantity of reporters, and the generally curious were on hand for what had been dubbed as REALLY the most important race ever. The hare was well aware that a number of friends and relatives, including some rabbits, mice and a couple of nasty looking rats were glaring at him with ill disguised skepticism. One of the rats even spoke everyone’s thoughts out loud. “Don’t screw up again this time, pal” he said.

The tortoise was awoken and joined the hare at the starting line. A chubby badger called out “ready, set, go” and they were off. The hare took off in a streak of speed, and within a few seconds was out of sight of the tortoise. He ran along the well marked race path (a deer trail in the woods) and began to pace himself a bit. He saw lots of tempting vegetables along the way, but he set his jaw (figuratively speaking) and without even thinking about stopping, he ran on.

Almost before he knew it he could see the finish line before him. A much larger crowd had assembled there, and they were cheering as he came into sight. He had a sudden temptation to stop and play some jokes just in front of the finish line, but all his training in discipline paid off and he resisted the urge. In a final show of glorious speed he crossed the finish line and ran into the waiting arms of three or four haresses who along with all the other assembled four legged animals acclaimed him as the one true champion. He was overjoyed and also greatly relieved. “I won” he said over and over to himself and everyone else, it felt great.

Meanwhile the tortoise was ambling along the path, steady as she goes as usual. He also didn’t think about stopping, but walked slowly and steadily on. It was a beautiful day. The sun was shining, the air was cool and fragrant with the smells of Spring. Off to the side of the path, the tortoise could see the early flowers blooming, and as he passed he noticed the same trees he had seen before, but he could see that some of them had changed slightly since the last time he had been this way. One lovely maple for example had lost some branches, probably in a wind or thunder storm.

He spoke now and then with some of the birds who flew by and a few deer who stopped grazing to watch his slow progress with curiosity and interest. Everyone he met greeted him courteously, and none made reference to the fact that he was far, far behind in the race. The tortoise was truly enjoying himself and feeling quite relaxed. At one point he had a wonderful idea, something that he was certain had never occurred to him before, and probably, he thought, had never occurred to any other tortoise, or possibly not even any other animal before. He grabbed this idea quite strongly so as not to lose it, and the more he thought about it the better it seemed. “How nice” he thought “to have such a shiny new idea on such a lovely day while walking through these beautiful woods.”

Quite some time later the tortoise saw in front of him a white line marked on the ground. As he walked over it, he saw two beavers and a muskrat, who had stayed behind to wait for his arrival, and he heard the muskrat  say “Sorry old man, I’m afraid you lost this time. The hare came by hours ago. The race is over.” The tortoise answered “Race? what race?”

Peer review is a critical process in modern science. Scientists with expertise in the right field judge the quality of a grant application or a manuscript submitted for publication in a journal. This judgment determines whether the grant will be funded, or the paper published. The work that scientists do to perform these reviews is generally done with very little or no recompense – it is considered to be an honorary task that is part of being a member of the scientific community. Without this kind of judgment by peers, science as we know it would be impossible.  Are there problems with this system? Yes, of course – but, like democracy, it beats all the alternatives.

The last job I had before retirement was at the NIH. I was one of the five Associate Directors of the Center for Scientific Review, the agency that manages the peer review of most of the 80,000 applications for research grants that come into NIH every year from scientists around the country.

In my role as Director of the Division of Physiological and Pathological Sciences, I had the ultimate authority to approve the academic and other well-respected scientists selected by my subordinates to be members of the peer review panels that would collectively review grant proposals on a range of biomedical research areas. I became an expert in all aspects of this kind of judgment.

The scientists who review grants make their judgments based on their own knowledge and experience, and their verdicts determine whether or not a scientist will get grant funds, which often has a major impact on the financial well being, reputation, and career path of the scientist who applied, as well as on others working in his or her lab.

Judgment is a major theme in the Bible.  It is prudent for all those making important judgments to take this responsibility very seriously. It is essential for a Christian to do so, since Christians must follow Scripture when it comes to moral issues like passing judgment. And what does Scripture say? in fact, should humans even act as judges of others, or is that only allowed for God? On first reading, it appears that Scripture answers yes to both alternatives. There are many verses that suggest it is wrong for people to judge one another, or that judgment is the prerogative of God alone:

Do not judge, and you will not be judged. (Luke 6:37)

…you who pass judgment on someone else…are condemning yourself, because you who pass judgment do the same things. (Romans 2:1)

 You, then, why do you judge your brother or sister? (Romans 14:10)

On the other hand, verses that suggest that people are allowed, and even encouraged, to exercise judgment also abound:

…render true and sound judgment in your courts.   (Zechariah 8:16)

Why don’t you judge for yourselves what is right?  (Luke 12:57)

Or do you not know that the Lord’s people will judge the world? (1 Corinthians 6:2)

So which is it? Are we supposed to judge or not? Actually,  I think that Scripture is clear. All the anti-judging verses apply to judgment of people. The pro-judge verses apply to judgment of what people do: their works and actions. A summary might be:

“Do not judge your brother, but do judge what he does and says.”

This solution is also consistent with the dilemma of a Christian making judgments about scientific proposals. Scientists who read the grants or papers of their peers make their decisions on the quality of the work presented – on the clarity of the ideas and their likelihood to be correct. While there is a minor aspect of peer review that relates to the individual applicant or author of a manuscript, even that judgment relates to what the individual has done before — it is not about the individual as a person.

I have never heard a grant reviewer say “The idea is good, the methods are fine, the applicant has a great track record, but I know him and he is a miserable person, so I vote no.” In fact such comments are strictly and explicitly forbidden.

As the new Editor-in-Chief of the magazine God and Nature, I am once again in the position of judging other people’s work. I find the wisdom from Scripture satisfying, because it allows me to make judgments on the work of others in humility and with the knowledge that I am following the will of God, as long as I avoid the trap of judging the basic worthiness of any member of the family of God’s people.

The subject of Judgment and Peer Review will be the focus topic for the Summer 2018 issue of God and Nature, and readers are encouraged to submit essays, stories, poems etc. I promise not to be too judgmental.

Just about a year ago, I put up a post called Finding My Faith, which presented a brief summary of  some of my reasons and experiences that led me from atheism to Christianity. Very recently, I posted a tweet that summarized my journey in two sentences and 25 words. That tweet has gotten over 8000 likes, over 5000 retweets, and resulted in my gaining almost 1500 new followers. It also led to numerous requests for more details about my direct experience with Jesus Christ, and how I came to faith.

To begin to answer questiobs about how I came to Christ, I have decided to repost most of my original piece on Finding My Faith, with some edits. If you would like to read more, please leave a comment in the comment section below with either your twitter handle or email. If you have already sent me a DM on Twitter, and I answered you, I will contact you directly.

I had an unusual upbringing for a Christian. My parents were dedicated materialistic atheists. They not only didn’t believe in God – they also thought that anything with a spiritual, psychological or non-rational quality was bogus. I grew up thinking that people of faith were lucky because they could fool themselves into believing that there was a loving God who would take care of them. I wished that it would be possible for me to become a believer. But it wasn’t. I had been too well trained in the dogma of materialism and rationalism to allow anything as weak-minded and logically indefensible as faith to penetrate my mind.

I became a scientist and embarked on a career in genetics and environmental health research, I began reading about physics, and found that some of the language of cosmology, quantum physics, and relativity didn’t sound that different from the language of mysticism. Intellectually, from a scientific point of view, I found the denial of the existence of transcendental mysteries in our universe and in our lives to be untenable. If Hawking can write of imaginary time, if we need to understand that space really bends, and that the uncertainty principle is true, how can we deny the reality of mystery? I also began thinking about some new ideas in my own field of genetics and evolution, and biology in general, that didn’t quite fit with the purely materialistic paradigm of strong atheism. I became convinced that there might be something….more. But thinking that there might be something out there and actually experiencing it are not the same thing. I remained an agnostic because I had no strong reason to believe anything else.

In my 40s I began accompanying a Catholic woman to church. I found it to be a surprisingly pleasant and non-threatening experience. It was a surprise because I had been taught that churches were the source of superstition, guilt, torment, and hostility.  The priest’s sermons were as surprising as the rest of the mass. The theme of this religion, which I had been taught was all about intolerance and power, seemed to be about love. I heard about the power of faith, forgiveness, and redemption, and about how all human beings are worthy of God’s love and how Jesus treated sinners (like me) as people worthy of His love and attention.

This didn’t make me a Christian – I was still on the outside looking in.  But I had  had several dreams that I later realized were direct calls from God, but did not understand when I dreamed them  They are all described in the book. Two of the dreams included the figure of Jesus Christ, but I did not realize that at the time.  In the last of these, I dreamt I was outside of a walled garden. I knew that in this garden there was to be found everything I had always been looking for, but there was no way I could climb over the wall to get in. I kept going around the walls, trying to climb up, falling down, and getting terribly frustrated. And then a man (Jesus) showed up, and said to me, “What’s wrong with you?” I explained I was trying to get into the Garden, but could not scale the wall. He smiled and said, “Then why not use the door?” and pointed to a door in the wall that I hadn’t seen before. I asked what I needed to do to gain entry. He answered, “Nothing, just open the door and go in.” So I did.

This dream and the others moved me, and helped me to break down my certainty that atheism was correct, and reinforced the sense I was getting after attending Church, that perhaps Christianity was a good thing. But still I resisted. How could I believe in something that might not be true? By now I knew that wanted to believe, I wanted to enter the garden, but was afraid to walk through the door, even with Jesus Christ holding it open for me. (When I had that dream I had not yet known the Gospel: “Seek and you shall find, knock and it will opened for you“).

I became a believer one day through the grace of the Holy Spirit. While driving on the Pennsylvania turnpike I had a direct experience of the power of the Lord, and it came from inside me out into the world. I had to pull over, stop the car, and for the first time in my life, I knew that God the Father, Jesus Christ, the Son, and the blessed Holy Spirit were as real as anything I could see or touch. I cried and prayed, and felt the joy of the Lord permeate my being, which has lasted to this day. Hallelujah and amen.

I have been asked many times to explain how so called “macro-evolution” works. There are of course many excellent books and articles online and off that cover this, but I thought it might be a good idea to have a blog post that explains it quickly and simply that I can refer to when asked. The following is adapted from a book manuscript (which might get published some day).

To see how macroevolution (the origin of new species) works, we can use a hypothetical animal, maybe one in the cat family. Let’s call it a lipard. And let’s say that there is a population of these large cat-like carnivores living on a large plain with plenty of prey animals. The lipards have gotten better and better at hunting thanks to several improvements (microevolution) in  vision, muscle strength, digestion of meat, and other traits. And all of these positive changes eventually got shared by the whole population of lipards, due to breeding and natural selection (like all examples of microevolution).

But now the population of lipards becomes divided so that there are two groups of lipards that cannot interbreed. Perhaps one group crossed a river, a desert, or a mountain range and couldn’t get back, or they just wandered so far away that it wasn’t convenient to find mates in the other group.

Now both groups of lipards continue to accumulate new genetic variations through mutations, but because they are no longer interbreeding with each other, the new variantions in one group do not spread to  the other group. With time, each group begins to differ in their variations. Now, for each  group, natural selection could choose different genetic variants to be successful than in the other group.

Its also possible that some differences in the two groups could arise by chance, and not have any important effects on survival (like slight differences in skin color). But the key point is that none of the changes will spread to the other group, because the two populations cannot interbreed.

With the passage of time,  different traits will appear  in one of the groups that are not found in the other. In one group, the skin could become darker, and in the other, males could develop a large mane of hair around their heads.  Both groups continue to change independently of each other, and after a long enough time, neither group resembles the original lipards. One group has become lions, and the other has become leopards.

They still have a lot in common, but they are now two separate species. Please note that no lion turned into a leopard or vice versa. Both lions and leopards share a common ancestral species, the lipard, which now no longer exists. It didn’t go extinct – it evolved. Lipards themselves had evolved from an ancestor that they had in common with tigers and snow leopards, and even further back with cheetahs and domestic cats. And they all became separate species the same way: population isolation, separate genetic changes in the separate populations, and continued evolution by natural selection. This is what Darwin observed among species of finches in separate islands of the Galapagos chain.

We can keep looking backwards in biological history. All the cat-like animals are descended from a no-longer-living ancestor shared with bears, wolves, hyenas, badgers, and other carnivores. If we keep going we will find a common ancestor for all mammals, and then all vertebrates, and so on. For an excellent book that describes all of this in beautiful detail, there is nothing to match The Ancestor’s Tale by Richard Dawkins.

Is there any evidence for this scenario of how the diversity of life arose? Yes, tons. There is so much evidence, both in fossil records and from genetics, that there is no doubt at all that the theory of evolution for the origin of species is correct (though perhaps not complete – see “New Ideas in Evolutionary Biology”).