Did a “Massive Genetic Study Reveal 90 Percent Of Earth’s Animals Appeared At The Same Time”? No, it didn’t.

The declaration in quotes is the title of an article in Tech Times reporting on a paper published in Human Evolution by Stoeckle and Thaler with the title Why should mitochondria define species? Not surprisingly, young earth creationists and others are linking this article all over the internet. I was first made aware of it by a friend, and then I read the original paper. The following is my analysis of that paper, originally posted in the Facebook group Celebrating Creation by Natural Selection (CCNS).

As expected, the Techtimes article completely misunderstood the original paper. It does not claim that 90% of all animal species began at the same time, 100,000 years ago, and it is in no way supportive of YEC. The paper, which I believe is poorly written and highly speculative, is an attempt to make sense of the fact that mitochondrial DNA bar coding is useful in identifying species. That fact is now consensus, and it derives from the fact that genomic differences between many species (like two worms or two similar insect species) can be quite small, but they are much greater in mt DNA (mt=mitochondria). The reason for this is that mtDNA has a far greater mutation rate than genomic DNA, since negative selection is not an issue (meaning a deleterious mutation in mt will not usually kill the cell in which it lives). So when two species are hard to differentiate by genomic sequence differences, they can be up to 2 or 3% different in their mtDNA. This also implies that there is very little variation of mtDNA within the individuals of any species. The purpose of the paper is to suggest hypotheses as to why the latter observation is true.

One possibility for explaining why mtDNA within a species shows less variation than between closely related species is that a particular species went through a population bottleneck followed by rapid expansion. A bottleneck can occur for several reasons, but generally involves a large decrease in the population, usually due to adverse environmental conditions. It can also result from migrations. Bottlenecks are very common during evolutionary history, as populations deal with all kinds of stressors. Bottlenecks are known to cause severe restrictions in DNA sequence diversity, both in genomes and mt. We know that humans went through a severe bottleneck between 70,000 and 150,000 ya. The authors propose that most other animal species also suffered some form of bottleneck within the past 100,000 or “several hundred thousand” years ago. That is one possible explanation for the relatively low intra-species mtDNA diversity seen in modern animals. Personally, I am not convinced by this explanation, since the genomic DNA diversity data does not seem to match, as far as I know. But even if this explanation is correct, it says nothing about all animals originating at the same time. What it might suggest is a large-scale environmental change (such as the start or end of an ice age) or several such changes affecting different species at different times, which we know happens continuously.

The authors of the original paper never discuss “origin” or beginning of species. They simply suggest that one or more bottlenecks have happened to a large majority of species within a relatively short time frame. While that explanation is far from consensus at the moment, even if it gains evidence, it does nothing to shake any part of evolutionary theory or our knowledge of how environmental change affects population genetics.

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Darwin’s Visit

The dentist did his best with my root canal, and I went home, took some pain killers, and fell asleep. I woke up still feeling drowsy, so I went out into the backyard for some fresh air. Sitting at the table under the big umbrella on the deck was Darwin. He gestured for me to join him. I sat down and told him I was a big fan. “Yes, I know,” he said. “I read what you wrote about me being in Heaven, and you’re right. I also do appreciate your finding that letter I wrote to Wallace” (See The Story of my Greatest Discovery).

This made me very happy, although I was already starting to realize I was dreaming. Still, how often does one get to chat with Darwin? So I just went with it.

“Where are your horses?” he asked me. “We don’t use horses anymore. We have cars,” I told him, and I led him to my old Toyota for a ride. Darwin was impressed. He expressed amazement that at such enormous speeds none of the cars bumped into each other, but I told him it does happen. We drove into the town, and he asked where the factories were, why the air was so clean, why the streets were not filthy, and then he figured it out (“Ah, yes, of course, no horses”). The dream (which by now it clearly was, even to the dreamer) then took on one of those snapshot qualities, where we made brief appearances at various localities: a restaurant, a hospital, a school, a university, and a biochemistry research lab.

Back on the deck Darwin began a long lecture, only part of which remained with me when I woke up. He was ecstatic at the things he had seen. I started telling him about WWII, terrorism, and global warming, but he waved me quiet. “Of course, I know all about those things. We try to keep up to date with all the disasters down here, and we do get regular updates from freshly arrived victims, you know.” But he told me that things like computers, cars, and cures had gone unnoticed, at least by him.

“You know, despite everything, you people have made a great deal of progress in the past century and a half. And I daresay I expect this trend to continue. If I weren’t already in Heaven and in the know, I might venture to say that there is the appearance of a divine hand in all of this” – with a large gesture he indicated my humble house, the small garden, the driveway and the street beyond. Then he stared at me. “You are a Christian, are you not?”

“I am.”

“Good fellow. I can see now where I went wrong. I know that bad things still happen, but a lot less than they used to. So, if we extrapolate forward a bit, it appears that God is correct (as usual), and the Kingdom will indeed come to Earth. Now I understand why Jesus is always in such a good mood. Well, I must dash. Very good to have met you, and all the best.”

And then I was alone… well, not quite, my wife was sitting quietly next to me. I resisted the urge to tell her all about my visit from Charles Darwin. I thought I would wait a bit and tell her along with all of you readers.

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Intrinsic Biochemical Intelligence

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.

 

 

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Darmarckian Evolution

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 19th 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 20th 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”.

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God and Nature, Spring 2018

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.

 

 

 

 

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The Tortoise and the Hare – The Rematch

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?”

 

 

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Judgment and Peer Review

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.

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