The Science of Atheism.

Atheism is simply the lack of belief in a god, or in a supernatural being. We hear that all the time, and it’s generally true, from a dictionary point of view. So are there no other beliefs or attitudes or philosophical world views that accompany the statement “I am an atheist”?

Let’s take a closer look. Atheists are a very diverse group, so nothing I say refers at all to all atheists. But there are some beliefs and philosophical world views that are commonly held by many (sometimes most) atheists, especially those who identify with the newer, more militant brand of atheism promoted by Krauss, Harris, Stenger, Dawkins et al.

Here is a partial list:

Free will and consciousness are delusions. Science (methodological naturalism) is the only legitimate epistemology. We are insignificant creatures living on a mediocre planet. There must be many far more advanced civilizations in the galaxy. All unsettled questions about the natural world (such as the origin of the universe and of life) will eventually be answered scientifically. All human emotional, moral and spiritual attributes are explained by evolutionary theory.

I know that many atheists will deny holding some or all of these beliefs. But others are continuously stating them in books, blogs, and articles by atheists. And the same themes are also repeated constantly on social media by less famous followers of the new atheist “creed”.

None of this should actually matter. There is no problem with a group of people all believing in some philosophical world view, even if some of them steadfastly refuse to admit it. But there is a problem when unspoken, unacknowledged presuppositions leak into the scientific enterprise. That is very dangerous. Religious (or anti-religious) agendas are as toxic for science as are political agendas. Most scientists have learned to reject these and stay away from the very risky business of allowing political or religious concerns to determine their research programs.

But sometimes  it seems that for a few scientists, the temptation to gain fame and public attention by supporting the atheist agenda has not been as easily resisted. It’s true that most of the time that we read some blockbuster story in an online or print rag about scientists unlocking the secret of life or proving the absence of God, the story turns out to be a terrible distortion of an honest scientist’s work. But sometimes it isn’t. Sometimes the scientists are actually doing research whose goal is not just better understanding of nature, but a stronger argument for atheism and against the existence of God.

Examples include research designs to gather evidence for a multiverse or any other explanation to counter the theistic argument of fine tuning of the cosmological constants; evidence against a true beginning of the universe, to counter the evidence that everything that exists came from nothing, which makes little sense in the absence of a Creator; evidence for life on other planets, to counter the false notion that Christians think the Earth was chosen by God as the only place for life and intelligence; evidence that our planet is an insignificant and minor dot in a vast universe which is teeming with much more interesting and valuable creatures and features, again to counter a false notion that Christians think the Earth is unique and the center of everything; evidence that human beings are nothing more that naked apes who acquired a few abilities (none of which unique to humans) that allowed them to conquer the planet. The purpose of the last example is to dismantle the Christian notion of Imago Dei. There have even been neuroscience experiments done to try to disprove the existence of free will.

These new anti-theistic research goals are a waste of time and resources. There is no need for science to fill these gaps in understanding in order to disprove religion. Faith in God cannot be disproven any more than the existence of God can be scientifically proven. I know that some atheists cannot grasp this, but scientists should be able to. Christians should not, and many do not use God of the gaps arguments as the basis of their faith. As a Christian scientist, I base my rational belief in God, not on what is unknown, but on what is known about our world. Like so many others, I know that new knowledge will never destroy my faith (whether it is the discovery of a multiverse or the natural mechanism for the origin of life, or the finding of alien life forms, or the final understanding of how humans came to be), but only enhance it. There is nothing that we can discover about the truth of how the world is and how it works that does not point to the glory of God.

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Whatever Works

Why doesn’t anyone speak Esperanto? For the same reason that communism failed, that there are always shortcuts, and that mutations are random.

The answer is that planned, designed systems never work as well as unplanned, natural systems that arise by some form of trial and error, often called natural selection.

Esperanto was a great idea: create a new language that has features of many of the existing language. All people would learn their own language and Esperanto, and everyone could then communicate with everyone else. But it never happened. People preferred to learn English, just as in the past they learned French or Spanish or Latin, or whatever was the dominant language of the times. But, we could argue, isn’t it more sensible for everyone to learn a common language that isn’t chosen because its spoken by some group that has temporal power and dominance? Yes, that makes sense. But so does the idea that its possible to have an economy where the production of cars or rolls of toilet tissue is planned in advance. Or that we should design the best routes so that shortcuts would be unnecessary.

It turns out that solutions that make sense are not always the best solutions. Sometimes this is because “making sense” is often a very complex thing. For example, in today’s world, it makes sense for a Dutchman to learn English, but much less sense for a typical American to learn Dutch (or anything else, except maybe Spanish). Americans, Britons, Canadians,  and other native English speakers don’t really need to learn other languages including Esperanto, so they don’t. Why therefore should a Dutchman or Norwegian who already speaks English bother to learn Esperanto? If a Norwegian wants to speak to an Italian, it’s much more likely that they both know English than that either of them has even heard of Esperanto.

The reasons for failure of planned economies (communism) or designed social structures (like teenage dance parties) is too complex for this discussion, but like language choice, they all stem from the same issue: Planned designs don’t work in complex systems.

Nowhere is this more obvious than in biology. A lot of things make sense when you first learn the details of biology and biochemistry, but just as many things don’t. SJ Gould loved to write about this, and the title essay in his collection The Panda’s Thumb is devoted to a discussion of biological features that really shouldn’t exist.

Most organisms have far more DNA than they need. And it seems very inefficient to keep replicating all of this useless chemical that serves no purpose. Except now we know that some of the “junk” DNA does actually serve some purpose, such as coding for regulatory processes, or as material for new genes. Another example can be found at the post “Occam was wrong”

Does this mean that biological creatures are somehow poorly designed? Yes, it does, and therein lies the strength of life on this planet. If life had been designed according to how we humans think it should have been, it’s very likely that life on Earth would have gone the way of Esperanto, communism, and all the other carefully designed systems of human beings.

Software engineers have learned this lesson and now use genetic algorithms that depend on random changes and a form of natural selection of the most optimum solution to solve very complex problems in software development.

Those who argue against the process of Darwinian evolution because it seems to negate the appearance of the intelligent design of life are therefore missing the point. The most intelligent way to design a well-functioning life form is through evolution by natural selection. It is far more intelligent than attempting to design a well-functioning bird that must also survive in an environment with well-designed insects, worms, trees, hawks, cats and people, If biology (and a lot of human culture) could be summed up in two words, they would be “Whatever works”.

I do believe there is an Intelligent Designer. But His intelligence is as far above the intelligence of the smartest human engineer. God, in His Divine intelligence, designed life not to look efficient to us, but to last. And natural selection was His tool to do it. Every living cell proclaims the Glory of God.

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Thank you…

Today, August 31, 2017 is the last day of the John Templeton grant that made this blog possible. BUT, it is NOT the last day of the blog. I will be continuing this blog into the future, and have no plans to stop or even slow down.

In fact, I have recently added three new pages to the blog, shown in the top banner.

Publications is an updated list of all of my publications divided into two categories: 1. Recent publications mostly related to science and faith issues, including links to the full papers.  2. A list of my scientific publications, from 1976 through 2010 (over 200). PDF reprints for any of them are available on request.

The second new page is Presentations, which includes the title, venue and a link to the actual video or audio (sometimes both) presentations. This list is not yet completely up to date. Stay tuned.

Finally, I have added a page called FAQs, which is intended as a summary of my views on many subjects related to my Christian faith and science. I link this page whenever I am asked one of the many common questions by someone on social media, to avoid having to answer the same question dozens of times. (This mostly applies to Twitter)

All of these pages will be updated periodically.

I also thought this milestone date would be a good time to summarize some of the facts and data about this blog over the two years of its existence. Since its inception there have been 118 blog posts, including 8 guest posts that have generated 13,964 views, 521 comments and 321 Likes. The blog has attracted 3,773 visitors from 64 countries including at least 20 views each from South Africa, Nigeria, China, Germany, UK, Australia, Canada, Austria, New Zealand, Colombia, and Denmark (and of course, the US). As if today the blog has 65 followers, and attracts about 30 views/day.

Thanks to all my followers, and all others who comment and/or visit this blog. I hope to continue to provide you with interesting material for the foreseeable future. .

I would like to close this post by especially thanking the John Templeton Foundation for funding this project (see the page “John Templeton Foundation” for details)  and in particular Paul Wason, Vice President, Life Sciences and Genetics, and Kevin Arnold, Program Officer, Life Sciences and Genetics, for their unwavering support, encouragement and friendship over the years.

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Guest Post: What the 2017 Eclipse Asks Us About Our Church Ministry, by Jennifer Secki Shields

Today’s guest post is by my friend and colleague, Jennifer Secki Shields. Jen was trained as a biologist, and was the long-term Director of Christian Education at Christ Crossman United Methodist Church in Virginia. More recently, she founded a new organization called Discovery and Faith http://www.discoveryandfaith.org/ which helps children and youth grow in their experience of God as they explore the world around them. Jen is also a member of the WesleyNexus Board of Directors, which is how we met.

 

I organized a viewing event for my Cub Scout Pack that was attended by ~75 friends and neighbors on the field behind our local elementary school. All of the school’s teachers came out, too. As the eclipse reached its maximum at 2:42 PM we could hear other groups cheering from their locations in our community. We added our chorus to theirs. For me, there is no question—that collective moment of awe and wonder was an act of worship, a joyous celebration of God’s creation!

It also is one more piece of evidence that tells us just how profoundly our culture is impacted by science. The AP is reporting that this eclipse was the most viewed and photographed of all time. Consider that many millions of Americans interrupted their busy lives to pause for this event. Millions even made roadtrips so that they could be in the path of totality. All of this, not just to witness an event described by science, but in complete trust that the scientists had accurately predicted the whole thing! And they had. You literally could have set your watch by this event. In my area, the eclipse began at 1:17 PM, and reached its maximum at 2:42 PM, exactly as predicted.

While all of this points to the power of science, this was clearly a spiritual experience for most viewers. This morning I heard a woman on the radio describe it this way, “It was like Christmas, but for only one time.” Another said, almost breathlessly, “I’ve never experienced anything like it.”

I left my viewing event singing to myself:

This is my Father’s world,
And to my list’ning ears
All nature sings, and round me rings
The music of the spheres.

Which leaves me wondering, did your church in any way acknowledge this historic moment in it’s Sunday worship services? In its children’s message or programming? In the pastor’s sermon? Did it seek to make a connection between scientific knowledge and biblical wisdom? Did we, the church, connect with our science-shaped culture? Or did we miss an opportunity to point to the living God?

The 2017 eclipse reaffirmed two things for me. First, that science is good at doing what science does, making accurate predictions and descriptions about the natural world—and the vast majority of Americans trust this. Second, that wonder—expressed by Christians and non-Christians alike—is alive and well. A church that seeks to be culturally relevant today will look for ways to engage positively with science so that it can bear more fruit for the kingdom of God.

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Our Scientific Publication on Gene Regulatory Networks for the John Templeton Foundation Grant

As part of our work for the John Templeton Grant #57657  “A New Biology of Spiritual Information” awarded to the Natural Philosophy Institute for the period from Sept 2015 through August 2017, my wife Aniko Albert and I published a paper in the Journal of Theoretical and Computational Science on the theory of gene regulatory networks. This is a peer reviewed, technical paper, and it describes most of the work we did to understand how the complexity of these networks could be understood.

We plan to put the scientific work described in this paper into a more theological or spiritual context in future publications, online posts, or other methods of public dissemination. While the official period of the grant is almost over, we intend to continue to work on several other aspects of the project (including this blog) for some time to come.

The paper is freely available online at this link

The complete citation for the paper is:

Garte S, Albert A (2017) The Role of Genotype in the Predictability of Dynamical Behavior in Complex Model Gene Regulatory Networks. J Theor Comput Sci 4: 155. doi:10.4172/2376-130X.1000155

I have posted below 1) the abstract from the paper, and 2) a description of the what the paper says in less technical language, including a summary of what we found. This also includes two figures from the paper. I will be happy to answer any questions about this research in the comments section of this post.

Abstract

Models of gene regulatory networks (GRN) have proven useful for understanding many aspects of the highly complex behavior of biological control networks. Randomly generated non-Boolean networks were used in experimental simulations to generate data on dynamic phenotypes as a function of several genotypic parameters. We hypothesized that the topological component of network genotype could be an obstacle to the discovery of mathematical formulas that can predict certain phenotypic parameters. Our data support that hypothesis. We quantitated the effect of topological genotype (TGE) and determined its influence on a number of dynamical phenotypes in simple and complex multi-gene networks. For situations where the TGE was low, it was possible to infer formulas to predict some phenotypes with good accuracy based on number of network genes, interaction density, and initial conditions. In addition to formulation of these mathematical relationships, we found a number of dynamic properties, including complex oscillation behaviors, that were largely dependent on genotype topology, and for which no such formulas were determinable. For integrated measures of gene expression state, we observed a variety of oscillation patterns, including stable, periodic cycling with a wide variety of period length, aperiodic cycling, and apparent chaotic dynamics. It remains to be determined if these results are applicable to biological gene regulatory networks.

Summary

Gene regulatory networks are some of the most important and most complex functional structures in biology. Such networks or circuits control which genes are active (actually being translated into proteins), and which are silent at different times, and in different cells. We have recently learned that the systems for control of gene expression are far more elaborate and convoluted than anyone could have imagined.

For a typical network, some genes become active (turned on) because they are the target of molecular switches made by other genes. At the same time, genes can also be silenced (turned off) by the action of other genes in the network.

The result of all of these interactions between genes is an incredibly complex web of control that is challenging to analyze in any detail.

A number of researchers have tackled the complexity of GRNs by using model networks and then analyzing their behavior by mathematical and algorhythmic methods. The idea is to try to come up with some general principles that might be applicable to actual real-world biological gene networks.

That is exactly the approach we took in our research. First we designed a system of gene regulatory networks, where (for example) there are 5 genes, each of which can have many different patterns of interactions with the other genes in the network. An example is shown in Figure 1.

One

FIGURE 1. Five-gene model regulatory network. A) Matrix array showing numerical values for each interaction between all genes. The effect of genes in the rows on genes in the columns is given by 0 (no interaction), +1, or -1. Self-regulation is not included. B) A diagram of the interactive network shown in A, with green arrows showing activating interactions, and red blunted arrows showing suppressive interactions. Green double arrows (between Genes 1 and 5 and between Genes 4 and 5) indicate reciprocal activation, and bicolor arrows (between genes 3 and 4, Genes 2 and 3, and Genes 2 and 5) indicate inverse reciprocal interaction, where one gene activates another gene that suppresses it. For example, Gene 2 suppresses Gene 3, activates Genes 1 and 5, is activated by Gene 3, and suppressed by Gene 5.

To construct these networks using a random number generator. Each network we made can be described by several characteristics. These include the number of genes that activate other genes, the number of genes that suppress other genes, and the exact pattern of how all the genes interact with each other, which can be described as the “topology” of the network. All these parameters together are called the genotype of the particular network. For 5 genes, there are more than 3 billion possible genotypes.

In some kinds of networks, the effect of the topological component of the genotype is very strong, while for others, it’s weaker. We found that when the topological component (the map of the network) was not as important as the quantitative parameters of the genotype (the number of activating and suppressing genes and the total density of gene interactions), it was possible to derive very accurate formulas that could predict the behavior of the networks as a function of time and other variables. But when the topological component was dominant, such equations only gave very approximate results.

An additional finding of our experiments using these models was that the time-related behavior of some very dense networks was extremely complex. We found that many of these networks showed an oscillatory pattern, as had been seen previously. But we also found that the details of the cycling oscillations were not very predictable, and at times became so complex as to resemble chaotic dynamic behavior. Figure 2 shows examples of oscillating patterns of gene expression with time produced in some of these networks.

Ten

FIGURE 2. The complex oscillatory patterns of three Compound networks.  A) Oscillatory period = 42 iterations.  B) An example of a commonly seen period of 60 iterations (present in about 13% of Compound networks). C) An aperiodic network, with an appearance of chaotic dynamics.

We don’t know yet if any of these results will be applicable to actual biological gene regulatory networks. But we do believe that the discovery of quantitative laws that govern the dynamic behavior of certain networks and the finding of the importance of network topology in determining how accurately these laws can predict the detailed behavior will have important implications for understanding how gene regulatory networks function to allow for some of the complexity that we know is everywhere in living creatures.

 

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The American Scientific Affiliation Annual Meeting

From July 26 to July 31, my wife, teenage stepson and I were in Colorado, first to visit an old friend in Boulder, and then to participate in the 76th annual meeting of the ASA in Golden (outside of Denver).

We started things off with a geology tour of the Front Range, including the Red Rocks, and Dinosaur Ridge. Knowing almost nothing about geology, I learned a lot, and was as impressed as everyone said I would be at the magnificent views and scenery of the Rocky Mountains. I have spent a lot of time in the Alps, and the Rockies are at least as grand.

The actual conference began the next day (Saturday the 28th). After a wonderful plenary lecture by climate scientist Katharine Hayhoe, I moderated the first Biological Sciences section of the meeting. Then after lunch, I went to the second Biology session, where I presented my talk on The Biochemical Teleology of Evolution. As I expected, there were some questions and comments, but not as much resistance to the idea of bringing teleology back into biology as I had anticipated. Parts of the talk included some of the material I have posted here recently about the Non-Conservation Principle in biology.

In the same session, Josh Swamidass, whom I have come to know from the Biologos blog, presented a fascinating idea about human genealogy (as opposed to genetics), in which he stated (correctly, in my view) that there is nothing contrary to science in believing that a single couple (Adam and Eve) are the progenitors of the entire human race, assuming that there were also other people alive outside of the Garden of Eden. That talk was very controversial, and there were many arguments and discussions about the idea, even after the session.

In the third and final Biological Sciences session, I was very happy to hear two talks focusing on the Extended Evolutionary Synthesis as a new and exciting development in evolutionary theory. Perry Marshall and Emily Ruppel Herrington (both friends of mine) presented these two talks, and again, a good deal of discussion was stimulated.

As in every conference, the best part is meeting old friends and making new ones. I was fortunate enough to meet several people whom I had come to know online from the Facebook group Celebrating Creation by Natural Selection (CCNS) and from my Twitter feed. Jeff Greenberg, John Pohl, Dana Oleskiewicz, and Kurt Wood were among those.

I was also thrilled to meet Leslie Wickman, the new Executive Director of ASA, and to catch up with lots of old pals in the science and Christianity movement, especially the previous Executive Director and old friend, Randy Isaac, who has guest posted on this blog (and hopefully will do so again).

One of the high points of the conference for me was the daily worship service, reminding all of us that science is derived from God’s creative majesty. On Sunday morning, Pastor Peter Hiett delivered one of the most powerful sermons I have ever experienced, bringing almost everyone to tears. His theme was “Daddy Love” and he talked about God’s love for His children in analogy with our love for our own kids. Not a novel theme, but the content and delivery were both stunning and overpowering.

On Monday morning, after an excellent plenary talk by Jim Peterson (the editor of the ASA journal Perspectives on Science and Christian Faith) about the ethical and religious implications of the new gene-editing technique called CRISPR, we drove our rented car back to Denver airport and flew home to Maryland, getting home about 11 PM.

I always get very tired after a conference, mostly from the intensity of the discussions, and the degree of thinking required. This one was no exception, but we were not able to take much rest. The next day we got up at 6 AM and went to our Church, where we had made a commitment to teach a science class at Vacation Bible School for the rest of the week. In addition, I had meetings to attend every night of the week after getting home.

So today, Friday, I am finally able to catch a breath, write and post this blog, and prepare for what comes next. But I am not complaining. Instead I thank God for the blessings of my life, which include the ability to remain active in the three things I love the most: science, my Christian faith, and the love of my wife (not necessarily in that order).

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Biological Non-Conservation and Natural Selection (Part 3)

The non-conservation principle (NCP) of life is directly responsible for the process of natural selection. We know that groups of organisms differ in their birth and death rates due to differences in the function of various forms of genes called alleles. This is generally what is meant by fitness. If Yp is the number of organisms with the p allele of a particular gene, and Yq is the number of organisms in a population with the q allele, then we have Eq 1:

EQ3.1

EQ3.1B

where dBp/dT is the birth rate for those with the p allele, and dDp/dT is the corresponding death rate. If we assume that either birth or death rates for both populations with different alleles are different, then

EQ3.2                                Eq 2

or vice versa. That is the definition of natural selection, where the strength of selection, S, is a function of the difference in population numbers containing the two alleles. This also stands for one definition of relative fitness, W (see next post for more discussion of fitness).  Eq 3:

EQ3.3

This follows the standard neo-Darwinian approach of assuming all evolutionary change is directly related to allele frequency differences in populations. However, to stay in keeping with more recent concepts in evolutionary theory, one could easily substitute any inheritable characteristic, such as epigenetic marks or alterations in gene expression regulation.

Note that if biological organisms obeyed a conservation law, such that

EQ3.4

as is true for matter and energy (see previous post), then

EQ3.5                        Eq 4

and S would always be 0. The conclusion is that the NCP allows for and gives rise to evolution by natural selection.

There are other physical and chemical entities that can be said to be created (born) and destroyed, such as reaction products of a spontaneous chemical reaction, meteorological events like a hurricane or storm,  geological events like volcanic eruption and island formation and loss, and all the cosmological events related to the birth and death of stars and planets. All these phenomena follow the law of conservation for matter and energy, (as does life)  and for all of them there are rates of birth and death that determine the rate of change of the higher level of organization, whether that is a spiraling storm, the life of a star, or the half-life of an organic compound in an aqueous solution.

And yet, biology is different, and one of the most important differences is found in the nature of the alleles we called, p and q. The existence of alleles implies a system of inheritance of characteristics that is not found in any other physical or chemical system. And it is the existence of genetic variation (alleles, or any other form of inherited genetic information) that makes natural selection (Eq 3) possible.

In the next post we will explore the relationship of biological variation to the teleology in biology.

 

 

 

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