Junk DNA and Evolution

Does evolution depend on a lot of junk DNA?
Does evolution depend on a lot of junk DNA?
In my previous post, I reviewed the book Naturalism and Its Alternatives in Scientific Methodologies. At the end of the review, I mentioned that the book suggested a conclusion for the famous ENCODE experiments that I had never considered. In case you are unaware, ENCODE is an international collaboration of scientists who want to find out exactly how much of the human genome is actually used by the human body. In 2012, they made the startling announcement that more than 80% of the human genome has at least one biochemical function. This flatly contradicts the evolution-inspired notion that the vast majority (up to 98%) of the human genome is composed of “junk DNA” and is not used for any purpose. Evolutionists have generally dealt with ENCODE’s conclusion in one of two ways. Some say that ENCODE’s definition of “function” is too broad, so what they call “functional DNA” is not really functional. Thus, the vast majority of human DNA is still “junk.” Others suggest that the concept of “junk DNA” isn’t vital to evolution to begin with, so ENCODE’s results (correct or incorrect) do not really relate to evolution.

I have always considered that those in the latter group have a very weak case. As Dr. John Sanford demonstrated a while ago, the “gold standard” digital simulation of evolution (Avida), requires at least 85% of the starting genome to be junk in order to produce any significant evolution. However, while reading Chapter 13 of Naturalism and Its Alternatives in Scientific Methodologies (written by Salvador Cordova), I learned about another argument against the idea that evolution doesn’t depend on junk DNA. It comes from evolutionist Dr. Dan Graur, who says quite plainly:

If ENCODE is right, evolution is wrong. (p. 234 of Naturalism and Its Alternatives in Scientific Methodologies)

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Naturalism and Its Alternatives in Scientific Methodologies

The cover of the book (click for Amazon entry)
The cover of the book
(click for Amazon entry)
What is the nature of science? Many think this is a fairly easy question to answer. Science is about making observations and then forming the most reasonable conclusions based on those observations, right? Well…that depends. There are many (myself included) who think that the scientific community as a whole artificially censors certain conclusions, because those conclusions don’t fit a criterion that has been imposed on science: that science can refer only to material causes. Because of this view, which is often called naturalism, many claim that science cannot deal with issues like purpose, will, the soul, or God. Of course, this flies in the face of science history, which shows us that the science we have today was formed by those who continually incorporated God into their scientific research.

The purpose of Naturalism and Its Alternatives in Scientific Methodologies is to explore how naturalism overtook science and how that error can be corrected. The book is actually a compilation of the proceedings of the 2016 Conference on Alternatives to Methodological Naturalism. As such, it is really a collection of essays written by multiple authors. Some of the authors deal with the problem of naturalism’s infection of science, others discuss how scientists can build alternatives to naturalism, and others make suggestions for how non-naturalistic causes can be used to guide research in certain fields.

But wait a minute. Science is about studying the natural world – doing repeatable experiments and coming up with conclusions that apply uniformly throughout nature. Doesn’t anything supernatural work against that? After all, if miracles can occur, doesn’t that mean I can’t trust my experiments? Couldn’t any result I get in the lab be the work of a capricious demon? Of course not, and the author of the second contribution to this book (Tom Gilson), gives us the obvious reason why.

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The Great Good Thing: A Secular Jew Comes to Faith in Christ

The cover of Andrew Klavan's book (click for Amazon entry)
The cover of Andrew Klavan’s book (click for Amazon entry)
In a previous post, I discussed Andrew Klavan’s conversion story and mentioned that he had written a book about it. I said I would read and review it when I had the chance. I read it a few weeks ago, but the book requires quite a bit of reflection to review, so I have only now come to the point where I can actually write my thoughts about it. It’s not that the book is hard to understand. It’s that the book is a real mixed bag.

First, let me say that Mr. Klavan is a masterful writer. When you sit back and think about the way that he is expressing his thoughts, you realize what an artist he is with words. However, what he says varies from shamefully self-indulgent to amazingly profound. There were times I got so annoyed with the self-indulgence that I nearly put the book away, but his flashes of brilliance kept me going. He says that his first draft was nearly twice as long as the final copy and that his wife helped him clean it up. I am glad she did, because I don’t think that his flashes of brilliance would have gotten me through nearly twice as many pages!

Now don’t get me wrong. I really am glad that I read the book, and I think that lots of people should read it. I am just warning you that there are times you will roll your eyes and think, “Please don’t give me another detailed account of another memory.” Of course, I understand the problem. He’s telling you about how he made the dramatic change from a Jewish person who didn’t believe in God to a Jewish person who started following God’s Son. That’s a remarkable change, and it requires a lot of backstory. I just think Mr. Kalvan gives you too much backstory. However, dealing with the backstory is well worth it, because the overall story is both compelling and important.

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Another Failed Evolutionary Prediction

A fossil cast of a Protoceratops nest (click for credit)
A fossil cast of a Protoceratops nest (click for credit)

According to the currently-fashionable hypothesis, dinosaurs evolved into birds. Indeed, some evolutionists take this to such an extreme that they say things like:

Birds Are Living Dinosaurs

While there are some evolutionists who disagree with this hypothesis, it is part of the current scientific consensus. Of course, for a hypothesis to be considered scientific, it must make predictions that can be confirmed by the data. The more its prediction are confirmed, the more reliable it becomes. The more its predictions are falsified, the less reliable it becomes.

Indeed, one of the reasons I consider the creation model to be very strong is that it has made several predictions which have been confirmed by the data (see here, here, here, here, here, here, and here, for example). The evolution model, however, has made many predictions that have been falsified by the data (see here, here, here, here, and here, for example).

The hypothesis that dinosaurs evolved into birds has been used to make a prediction about the time it took for dinosaur eggs to hatch, which is typically referred to as the incubation period. We can’t directly measure the incubation period of dinosaur eggs, but many evolutionists have assumed that it must be similar to that of birds, which is quite different from that of reptiles. For example, Dr. Kenneth Carpenter wrote a book entitled, Eggs, Nests, and Baby Dinosaurs: A Look at Dinosaur Reproduction. On page 200, he suggests that the incubation period of dinosaur eggs should be similar to that of birds. He shows how bird egg incubation period varies with mass and then writes about a particular dinosaur egg:

…with an estimated live weight (i.e., as it might have been 70 million years ago) of 152 g, would have an estimated incubation time (from time of egg laying until hatching) of thirty-five days.

Similarly, on page 266 of Biology of the Sauropod Dinosaurs: Understanding the Life of Giants, we read:

The amount of time necessary for a dinosaur embryo to mature to the hatching stage may never be known with certainty, but it can be at least roughly estimated by a model developed by Rhan and Ar (1974) for birds. On the basis of comparisons with extant birds that have, in contrast to modern reptiles, a rather constant incubation temperature of about 40 oC, a dinosaur egg of 1.5 kg – the size of an ostrich egg – would require an incubation time of about 60 days to hatch.

The latest research indicates that such predictions aren’t anywhere close to being correct.

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What Happens to the Mind When the Body Can’t Communicate?

A version of the brain/computer interface cap used in the study (click for credit)
A version of the brain/computer interface cap used in the study (click for credit)

More than five years ago, I sat by a hospital bed where my Aunt Kay lay dying. Unlike my father, she was completely uncommunicative on her deathbed. She never made any purposeful physical movements, and despite repeated requests, she never indicated that she was aware of what was going on around her. I remember sitting there wondering whether or not she was “in there.” Was she able to hear the words of love people were sharing with her, or was she, for all intents and purposes, already gone? While I am here on this earth, I will never have the answer to that question, but a recent scientific paper indicates that in at least some cases, completely uncommunicative people really are still “in there.”

In this case, the study was done on four patients with advanced amyotrophic lateral sclerosis (ALS). Their cases are so severe that they are described as being in a complete locked-in state. This means that they cannot make any voluntary movements at all. They can’t even move their eyes. As a result, they have no way of letting others know what they think or feel. One of the patients had been unable to reliably communicate with anyone for six years prior to the study. Two of them had been in a similar uncommunicative state for two years, and one of them for several months.

The researchers outfitted each of the patients with a cap similar to the one pictured above. It could communicate with a computer that recorded measurements related to the physical workings of their brains. The researchers then instructed the patients that they would be asked several yes/no questions over the course of the study. Some would have answers that could be verified. Some would be “open” questions for which only the patient knew the answer. The patients were asked to strongly think “yes” or “no” (actually, “ja” or “nein” since the study was done in Germany) in response to each question. They were specifically told not to “picture” their response. They were told to only think it.

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Politics Poison Science

In 2015, the NOAA published a "scientific" paper for what appear to have been political reasons.  We now know the data used are false and should have never been published.
In 2015, the National Oceanic and Atmospheric Administration (NOAA) published a “scientific” paper for what appear to have been political reasons. We now know the data used are false and should never have been submitted for publication.

From the days I started doing scientific research, I have seen that politics play far too great a role in science. Some of this stems from the fact that most basic research is funded by the federal government, and since politicians control the money, they inevitably exert influence on what kind of scientific research is done. Over the years, however, I have observed a nasty, growing trend of scientists’ own political views influencing the way they handle data and communicate their results. In some fields, the political influence is worse than it is in others, and climate science might be the most politicized field of them all. A story posted on Dr. Judith Curry’s blog is the latest in a series of revelations that show us just how bad this has become.

Starting in the late 2000’s, those who had been studying worldwide temperatures noticed that the average temperature of the earth was not increasing. This was troubling for those who believed in human-produced global warming, since the models upon which they base most of their conclusions suggest that the earth’s average temperature should be increasing with increasing levels of carbon dioxide. As time went on, this lack of warming became more and more difficult to understand under the human-produced global warming paradigm, and critics of the paradigm started calling it “The Pause.”

In 2015, however, scientists from the the National Oceanic and Atmospheric Administration (NOAA) produced a report that was published in Science, one of the world’s most prestigious scientific journals. According to this report, “The Pause” was an artifact of the way earlier temperature analyses were done. When those analyses were “corrected,” there was no “Pause.” As shown in the NOAA-generated graph above, the trend of global warming had remained constant since the early 1950s. While slower than predicted by the models, it had not slowed down in recent years at all. As a result of its conclusion, this paper became known as the “Pausebuster” paper.

Interestingly enough, the Pausebuster paper was published about six months before the United Nations Climate Change Conference in Paris, France. Critics of the paper noted this timing and argued with the conclusions. In fact, another prestigious scientific journal, Nature, published a paper in 2016 (after the Paris conference) that strongly argued against the conclusions of the Pausebuster paper. We now know for certain that this 2016 paper is correct, and that the scientists who produced the Pausebuster paper disregarded the NOAA’s protocols in the process of producing their paper. How do we know this? Because the scientist who wrote some of those protocols has finally spoken out.

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No Doubt About It: These Proteins are From Dinosaurs

Fossil of a Brachylophosaurus at the Children's Museum of Indianapolis.  (click for credit)
Fossil of a Brachylophosaurus at the Children’s Museum of Indianapolis. (click for credit)

In 2005, Dr. Mary Schweitzer shocked the paleontology community by reporting that she had found soft tissue in a Tyrannosaurus fossil that was thought to be 65 million years old. Since then, numerous other cases of soft tissue in dinosaur fossils have been reported (see here, here, here, here, and here, for example). Currently, the “record holder” for soft tissue is a worm fossil that is supposed to be 550 million years old!

While such discoveries have been met with skepticism, the overwhelming evidence points to the fact that there is soft tissue in many fossils that are supposed to be millions of years old. Of course, the next obvious issue to address is the chemical makeup of these soft tissues. Are the large biomolecules that we expect to find in soft tissue there? Are they intact or severely decayed? After all, most proteins are expected to decay significantly in as “little” as 30,000 years. Despite this fact, some of these fossils contain what appear to be intact proteins.

Now, of course, there is always the possibility of contamination. Fossil collection isn’t the cleanest of pursuits, and proteins are found pretty much everywhere on the planet. Thus, it is possible that the proteins which have been discovered in dinosaur bones aren’t really from the dinosaurs. However, two recent studies indicate that contamination cannot be the explanation. These proteins are real, and they really are from the dinosaurs themselves.

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Jay Wile, From a Student’s Perspective

A "portrait" of me, drawn by Jessica M.
A “portrait” of me, drawn by Jessica M.
I love hearing from students after they have taken a course or two from me and then gone on to pursue their goals. I enjoy each report and am thrilled that my courses meant so much to them. I do have to admit, however, that I enjoy some reports more than others. Some students credit me for their love of science, and that means the world to me! Others suggest that they couldn’t have been successful in pursuit of their goals without my courses. I tend to doubt that, but I appreciate the sentiment. Some students say that my courses have helped them in their spiritual life, and that means the most. There are times, however, that I get a report that is both meaningful and downright hilarious, at least to me! Such was the case a few days ago, when I got an email from Jessica M.

She wrote to tell me that she took my general chemistry course (which is out of print – I recommend using this one now) and my advanced chemistry course several years ago and is now in college, pursuing a degree in nursing. She says that college chemistry is going well, and it is bringing back a lot of good memories, so she wanted to thank me for being an integral part of her homeschool-high school years. Of course, that meant a great deal to me. However, I have to admit that I was more intrigued by something else she wrote:

As a homeschooler, you were one of my first “favorite professors” (next to my parents and Andrew Pudewa). Extrapolating from your often-humorous, lighthearted writing style, I invented a jovial stickman-character of you who often appeared in the margins of my books to make comments (together with the three Chemistry Nerds and Mr. Mole).

If you have ever experienced a class with Andrew Pudewa, you would know that it is no insult to finish behind him in a student’s “favorite professors” list, but that’s not what really intrigued me. I wanted to learn more about this “jovial stickman-character,” so I asked her if she would mind sending me some examples, and when she did, I spent the next several minutes laughing out loud!

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The Future of Creation Science is Bright

Dr. John Sanford (right) and me (left) at the Creation Science Fellowship Meeting in Costa Mesa, California.
Dr. John Sanford (right) and me (left) at the Creation Science Fellowship Meeting in Costa Mesa, California.

This past weekend, I had the opportunity to walk among giants…well…at least figuratively speaking. I got to participate in panel discussion with Dr. Steve Austin, Dr. John Baumgardner, and Dr. John Sanford. Anyone who has spent much time researching the origins issue will recognize at least one of these individuals, as they are all excellent scientists who write and do research from a creationist perspective. I didn’t think I belonged on the panel, since I consider them all to be much more accomplished and talented scientists than me, but the people at the Creation Science Fellowship in Costa Mesa, California seemed to think I could contribute to the discussion, so I was included.

While the panel discussion was well attended and very productive (I will discuss it a bit in a moment), the most exciting aspect of the trip for me was meeting Dr. Sanford. He is an incredibly gifted geneticist. For example, he co-invented the “gene gun,” a device that can introduce DNA from one organism into a completely different species of organism. He has also done some excellent creationist research (see here and here, for example) and has written what I consider to be the best book about genetics and evolution, Genetic Entropy and the Mystery of The Genome. I have discussed parts of it in previous posts (see here and here).

I was also thrilled to hear about an organization he is leading, which is called Logos Research Associates. It is a group of scientists who are committed to doing original, cutting-edge scientific research from a creationist perspective. Their current projects investigate issues in oceanography, genetics, geophysics, and geology. The more I discussed his organization and its projects, the more excited I became. The projects are incredibly interesting, and the way they are addressing the scientific issues involved is spot-on. He told me about a couple of papers that are in the process of being finalized right now, and once they are published, you can bet that I will write about them.

Scientists like Dr. Sanford and organizations like Logos Research Associates make me think that the future of creation science is very bright.

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College Professors’ Impressions of Homeschool Graduates

A happy college graduate (click for credit)
A happy college graduate (click for credit)

Many of my readers probably know that I started working with homeschoolers because of my experiences with homeschool graduates when I was on the faculty at Ball State University. As a group, they were not only academically superior to their peers, but they were also significantly more well-adjusted. I often share this fact when I am speaking to homeschool audiences, so it didn’t surprise me when a homeschool blogger (Michelle) sent me some questions about my experiences with homeschool graduates at the university level. As I indicated to her, I have experienced homeschool graduates at both a secular university (Ball State) and a Christian university (Anderson University). Based on my experiences, I can state with some confidence that, on average, homeschool graduates excel at the university level, be it in a secular or Christian environment. Several studies back up those experiences (see here, here, here, here, and here).

Michelle told me that she was writing a blog post about professors’ impressions of homeschool graduates, and she asked me four specific questions. I answered them as best I could and then (like many things) promptly forgot about it. Yesterday, I received another email from Michelle, telling me that she had finished the project and had published her post. After reading it, I decided that I had to share it. I think it provides some really valuable insights, especially for parents who are currently homeschooling and want their children to pursue higher education.

Unlike the studies that I spend a lot of my time discussing, the results of her survey of college professors is not scientific. It has a tiny sample size and makes no attempt to be representative of the population of college professors as a whole. Nevertheless, it is incredibly valuable, because the college professors who were surveyed offer some excellent advice to homeschooling parents, and they provide perspectives about homeschool graduates in higher education that would be hard to measure in a more scientific survey.

I strongly encourage you to read the entire article, but I do want to offer a bit of “color commentary.”

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