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)
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.
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.
A view of the Ark Encounter (click for a larger image)
In early August, I toured the Answers in Genesis Ark Encounter. Overall, I was impressed with the facility, and I thought that regardless of your view on origins, it would be a very interesting place to tour, if you can afford it. Of course, there are those who aren’t as favorably disposed towards the Ark Encounter, and they have a different view. Because I try to read all sides of an issue, I visited several anti-Ark websites prior to and after my visit, and many of them claimed that The Ark Encounter wasn’t getting a lot of visitors (see here, here, here, and here, for example.). I didn’t quite understand that, because the day I went (a Thursday in August), the place seemed pretty crowded. As I noted in my article, I had to wait 20 minutes to see one exhibit, because of the long line of people.
That’s why I was interested to read the December 31st entry on Ken Ham’s Blog. In that post, Mr. Ham lists seven ways that God blessed Answers in Genesis in 2016, and number three is:
Number of guests at the Ark. We’ve seen nearly 500,000 guests visit the Ark Encounter since it opened. Almost half a million people—including skeptics—have been encouraged to trust God’s Word and the gospel through the Ark!
The Ark Encounter opened on July 7, 2016. As of December 31, then, it had been open for a bit less than half a year. Thus, it seems likely that by July 6, 2017, the Ark Encounter could have as many as a million guests, perhaps more.
Climate Scientist Dr. Judith Curry
(click for source)Dr. Judith Curry holds an earned Ph.D. in geophysical sciences from The University of Chicago. For the past 14 years, she has been on the faculty at the Georgia Institute of Technology, and for the majority of that time, she was the chairperson of the School of Earth and Atmospheric Sciences. She has authored 186 peer-reviewed scientific papers and has two books to her credit. By any objective measure, she is a giant in the field of climate science.
I wrote about Dr. Curry more than six years ago, when Scientific American branded her a heretic. What was Curry’s heinous crime against science? She didn’t toe the party line when it came to global warming. She didn’t claim that global warming wasn’t occurring, and she didn’t claim that people aren’t responsible. Instead, she simply started stressing the real uncertainties involved in climate science. That, of course, is an unpardonable sin, and as a result, she is routinely demonized by those who know significantly less than she does about climate.
Why has she decided to resign, even though she has not reached traditional retirement age? She discusses this on her blog, and I encourage you to read the entire article. Like most of the entries on her blog, it is thoughtful and revealing. She mentions several factors that have contributed to her resignation, and then she says this:
A deciding factor was that I no longer know what to say to students and postdocs regarding how to navigate the CRAZINESS in the field of climate science. Research and other professional activities are professionally rewarded only if they are channeled in certain directions approved by a politicized academic establishment — funding, ease of getting your papers published, getting hired in prestigious positions, appointments to prestigious committees and boards, professional recognition, etc.
How young scientists are to navigate all this is beyond me, and it often becomes a battle of scientific integrity versus career suicide… [emphasis mine]
The sad fact is that her observations are 100% accurate, and they can be applied to at least one other field of scientific inquiry – the investigation of origins.
The stringy stuff hanging on this tree is a lichen from the genus Bryoria.
(click for credit)If you have been reading this blog for a while, you know that I am fascinated by mutualism – the phenomenon where two organisms of different species work together to benefit one another (see here, here, here, here, and here, for example). Creationists expect such relationships to be common throughout nature, and at least one line of research seems to indicate that some organisms are designed to produce them. I suspect that we understand very little about this amazing process, and it is probably more common than most scientists think.
Consider, for example, the longest-studied mutualistic relationship. Way back in 1867, Swiss botanist Dr. Simon Schwendener proposed that a lichen (like the one pictured to the left) is not a single organism. Instead, it is composed of two different organisms, a fungus and an alga (the singular form of algae), that work together so that each benefits. His hypothesis was rejected by the scientific consensus, but as has been the case throughout the history of science, the consensus was demonstrated to be wrong, and Dr. Schwendener was vindicated. Nowadays, the lichen is one of the most common examples given to explain the concept of mutualism. The alga does photosynthesis and shares its food and oxygen with the fungus, while the fungus supports the alga and supplies it with water and salts.
You would think that since Dr. Schwendener proposed this mutualistic relationship nearly 150 years ago, scientists would know pretty much everything there is to know about lichen. However, there was one major mystery that hadn’t been solved over that entire timespan – how can genetically similar lichen be so wildly different? The picture above, for example, is of a specific lichen, Bryoria fremontii. Another lichen from the same genus, Bryoria tortuosa, is composed of the same species of fungus and the same species of alga. From a genetic standpoint, the fungus and alga in both lichens are virtually identical. Nevertheless, one lichen is brown while the other is yellow. In addition, one produces a chemical known as vulpinic acid, while the other does not.
How can two lichen composed of genetically-identical partners look and behave so differently? We may now know the answer, which has been hiding in plain sight for almost 150 years!
A colony of bacteria similar to the one analyzed in the study being discussed. (click for credit)Back when I went to university, I was taught (as definitive fact) that bacteria evolved resistance to antibiotics as a result of the production of antibiotics. This was, of course, undeniable evidence for the fact that new genes can arise through a process of mutation and natural selection. Like most evolution-inspired ideas, however, the more we learned about antibiotic resistance in bacteria, the more we learned that there was a problem. It turns out that some cases of antibiotic resistance in bacteria were not caused by antibiotic-resistant genes. Instead, they were caused by the deterioration of genes that exist for other purposes. For example, the Anthrax bacterium can develop resistance to a class of antibiotics called quinolones, but it is the result of a mutation that degrades the gene that produces gyrase, the enzyme that those antibiotics attack. This allows the bacterium to survive the antibiotic, but the degraded gyrase gene causes the bacterium to reproduce much more slowly.
There are, however, specific genes found in bacteria that do produce proteins which fight antibiotics. It was generally thought that these genes arose through mutation and natural selection in response to our development of antibiotics. However, we now know that this just isn’t true. Antibiotic-resistant genes existed long before people developed antibiotics. I first wrote about this more than five years ago, when researchers found bacterial, antibiotic-resistant genes in permafrost alongside mammoth genes. Obviously, people weren’t making antibiotics when mammoths were alive. Thus, those genes existed long before human-made antibiotics. Later, I wrote about researchers who found bacterial, antibiotic-resistant genes in fossilized feces from the Middle Ages. Once again, this shows that antibiotic-resistant genes have been around long before our development of antibiotics.
Now an even more impressive study has been released. In it, researchers analyzed the DNA of a bacterium from the genus Paenibacillus. These bacteria form colonies, such as the one shown in the image above. The colors in the image indicate the density of bacteria – the brighter the yellow color, the higher the density of bacteria. While this genus of bacteria has been found in many, many environments, the specific species analyzed in the study was special: it has been living in a cave that has been isolated from the modern world. In fact, the cave is so isolated that no animals had ever ventured into it. When the researchers analyzed the DNA of this bacterium, they found all sorts of antibiotic-resistant genes.
Electron microscope image of three soft bone cells from a dinosaur fossil
More than three years ago, I wrote about the sad story of Mark Armitage, a gifted scientist who has become an expert in microscopy. In addition to running his own microscope company, he also worked as the Manager for the Electron and Confocal Microscopy Suite in the Biology Department at California State University Northridge. While on a fossil dig in the Hell Creek Formation in Montana, he discovered a 48-inch Triceratops horn. When he and his colleague soaked it in weak acid to remove the mineral components, they recovered soft, brown tissue.
If that’s not exciting enough, he also examined the fossil with a scanning electron microscope, and he found actual bone cells! Not only that, he saw no evidence for mineralization in the cells. In other words, he wasn’t looking at cells that had gone through petrifaction. He was looking at cells that still had their original components. So not only had he found soft tissue in the fossil, he had found soft cells!
Obviously, this kind of find is amazing. Not surprisingly, he and his colleague, Dr. Kevin Lee Anderson, wrote a report on their discovery so that other scientists could learn from it. The report was published in the peer-reviewed, secular journal entitled Acta Histochemica.
Not long after that, the Darwinian Inquisition struck. He was fired from his position at California State University Northridge. As I reported previously, he decided to sue the university. Why? According to him, one faculty member stormed into his lab and shouted:
We will not tolerate your religion in this department, or your creationist projects either!
Armitage thus concluded that he was being discriminated against based on his religion.
Apparently, he was right, because his case has been settled, and he says that he is very pleased with the result.
The centromere is the point at which a chromosome and its duplicate attach during cellular reproduction.
(click for credit)Uninformed people often say that creationism cannot make testable predictions. Since testable predictions are a necessary part of any scientific theory, these people claim that the creationist view isn’t scientific. Of course, nothing could be further from the truth! Creation scientists regularly make testable predictions, many of which have already been verified by further scientific research (see here, here, here, here, here, and here).
One of the more stunning examples of a confirmed creationist prediction is given by the nature of DNA. Since the 1970s, evolutionists have taught (as an indisputable fact) that the majority of the human genome is made up of useless stretches of nonsensical sequences which have been collectively referred to as “junk DNA.” However, in a Herculean study of human DNA, the ENCODE team demonstrated that a minimum of 80% is used by the cell and therefore should not be referred to as “junk.” One of the scientists on the team (Dr. John A. Stamatoyannopolous) stated:
I don’t think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance…
Actually, there were several scientists predicting this very result! Creationists have been doing so for years.*
Well, now that we know the vast majority of the human genome is functional, some scientists have removed the evolutionary blinders from their eyes (at least when it comes to the nature of DNA) and have begun to look at regions of the DNA that scientists have been assuring us could not possibly have any function whatsoever. When they study such regions, they (not surprisingly) find that those regions do have a function, and it is often a very important one.
James Tour is a giant in the field of organic chemistry.A few days ago, a reader asked me to review an article by Dr. James Tour, as well as a video of a talk that he gave. I was initially hesitant to do so, because Dr. Tour is a giant in the field of organic chemistry. For example, he is the T. T. and W. F. Chao Professor of Chemistry at Rice University. For those who aren’t familiar with the academic structure of universities, only the most elite professors are appointed to a position that is named in honor of someone else. This is called an “endowed professorship,” and anyone who holds such a position is in the upper echelon of academia. He has won several awards for his outstanding research accomplishments, including being named by Thomson Reuters as one of the top ten chemists in the world in 2009. Not only is his research outstanding, but he is also an excellent teacher, having earned the George R. Brown Award for Superior Teaching at Rice University in both 2007 and 2012. What could I possibly add to the words of someone so knowledgeable and distinguished?
After reading the article, however, I do think I have something to offer. Because of the nature of what he is trying to discuss, his article is very, very technical. There were times, quite frankly, when my eyes glazed over a bit. I didn’t listen to a lot of the video (it seems to cover the same ground as the article), but it is also quite technical. For those who do not have the fortitude to make it through such a technical article or talk, I thought I could summarize it.
The “take home” message is straightforward: We have no idea how some of the most basic molecules necessary for life could have been produced by unguided processes. Why does Dr. Tour feel compelled to write a detailed article making a statement that, in my mind, is quite obvious? He explains:
Those who think scientists understand the issues of prebiotic chemistry are wholly misinformed. Nobody understands them. Maybe one day we will. But that day is far from today. It would be far more helpful (and hopeful) to expose students to the massive gaps in our understanding. They may find a firmer — and possibly a radically different — scientific theory. [Note that “prebiotic chemistry” refers to the chemistry that occurred on earth before life existed.]
Poor assumptions can lead to myths instead of facts (image from shutterstock.com by Thinglass)I am always on the lookout for experiences that can be turned into a “teachable moment.” Over the past two weeks, I have had two such experiences, so I thought I would write about them. The first one was a result of my article entitled Reflections on the Ark Encounter, which is a positive review of the latest attraction produced by Answers in Genesis. The day after it was published, I got a Facebook message from someone who had shared my post with a friend of hers. In reply, this friend asked if I was a “real” scientist. She assured him that I was and shared my Facebook page with him. She was rather taken aback when her friend sent her the following reply:
A mimeographed “PhD” from whatever fundamentalist “college” he sent his box tops to is not qualification to shine a real scientist’s shoes, let alone make claims about the natural world. Further, any parents who buy into this complete fiction, and indoctrinate their kids in this manner, are guilty of emotional and mental child abuse, and in my opinion should be prosecuted. I cant think of a better way to sabotage a child’s future in a modern, scientific and technological society.
This didn’t surprise me, of course. I am used to having my credentials questioned and being insulted because I don’t slavishly “toe the line” when it comes to today’s scientific consensus. That comes with the territory. Indeed, Dr. Dan Shechtman was asked to leave his research group because he dared to question the scientific consensus. Of course, the data eventually proved him to be correct and the scientific consensus to be wrong. However, that was until after being ridiculed as a “quasi-scientist” by one of the greatest chemists who has ever lived!
