Category: Evolution

Microscopic Analysis of Dinosaur Soft Tissue Casts More Doubt on Proposed Preservation Mechanism

The dark mass near the center is the cell body of a dinosaur bone cell. The various “arms” extending from the body are its filipodial extensions. (click for credit)
I have written a lot about soft tissue found in dinosaur fossils and other fossils that are supposed to be millions of years old (see here, here, here, here, here, and here, for example). Right now, the best work being done on this issue comes from the Dinosaur Soft Tissue Research Institute, which is run by microscopist and young-earth creationist Mark Armitage. Without the help of government grants, he and his colleagues have produced some truly incredible work. Their latest contribution was published in Microscopy Today, and it strengthens the case that these fossils cannot be millions of years old. As always, I encourage you to read the article in its entirety, but here is my “color commentary.”

First, the article shows more incredible, delicate structures that would not be expected to survive any preservation process that would protect them for millions of years. For the first time in the scientific literature, there are two excellent pictures of dinosaur vein valves (Figures 2 and 3), features that are so delicate they are hard to extract from animals that have just recently died. In another first, he shows a nerve from the same fossil (Figure 6). In that nerve, you can see the delicate Bands of Fontana, structures that are unique to nerves.

He also shows a bone cell from the same fossil (Figure 7). While bone cells from dinosaur fossils have been published in the scientific literature, this particular one is very important. Bone cells have characteristic structures called filipodial extensions that are remarkably thin (widths of less than 200 billionths of a meter). The bone cell shown in their study has a filipodial extension that is 24 millionths of a meter long. That doesn’t sound like much, but it is about 30% longer than any other dinosaur filipodial extension found in the literature. This is important, because its length is more than 100 times its width. Think about a structure with those dimensions made out of soft tissue. It would be ridiculously fragile, yet there it is in a dinosaur fossil!

Second, and more importantly, he shows that the current explanation evolutionists have for the preservation of soft tissue in dinosaur fossils doesn’t work. Dr. Mary Schweitzer was the first to give strong evidence for the existence of soft tissue in dinosaur fossils, but she is committed to an evolutionary view. As a result, she needs to find an explanation for how such tissue could survive for millions of years. Seven years ago, she published a study in which she hoped to show that iron from the blood of a dinosaur could produce certain reactions that would preserve the tissues. I wrote about her explanation at the time and how it didn’t seem to make sense based on what we knew. Later on, better chemists than I wrote a detailed analysis about how her explanation is inconsistent with the data.

This new paper demonstrates rather conclusively that Schweitzer’s explanation doesn’t work for the fossil being discussed. Armitage and his colleague (Jim Solliday) search the filipodial extensions of bone cells that are found right outside a canal that held a blood vessel. Since the cells are so close to what was a blood vessel, and since the filipodial extensions are so delicate, those iron-induced reactions should produce noticeable effects on the filipodial extensions. He shows that those effects are not present. Thus, it is unlikely that such reactions happened at all in the fossil.

Also, in her study, Schweitzer took great pains to prevent blood clotting so that iron from the blood could be distributed throughout the soft tissue she was trying to preserve. However, Armitage and Solliday present strong evidence for massive blood clotting in their fossil. This would prevent iron from being able to promote any tissue-preserving reactions. While their evidence is strong, however, it is not conclusive. Thus, as they suggest, more research needs to be done.

The Dinosaur Soft Tissue Research Institute is on the forefront of this issue in science, and they are doing it without the massive government grants available to organizations who are desperately trying to fit the data into an evolutionary framework. If you have the means, I suggest that you make a donation to keep science progressing in this area.

Did This Bird Go Extinct and Re-Evolve? I Doubt It.

A flightless Railbird on the Aldabra atoll in the Indian Ocean (click for credit)

Over the past few days, several people have sent me articles like this one, which makes a rather fantastic claim:

The Aldabra white-throated rail bird was declared extinct, a victim of rising sea levels almost 100,000 years ago.

However, the flightless brown bird has recently been spotted – leaving scientists scratching their heads as to how – and why – the species has come back to life.

What do you conclude from reading that? The article seems to be saying that no one had ever seen this bird before; it was only known from the fossil record. Now, however, living versions of it have been seen, and how they came back from extinction is a mystery. Unfortunately, like many “science news” stories, this one distorts the science to the point that it is deceptive and misleading.

The science that is being distorted comes from a study published last year. A responsible article that describes the study can be found here. While the study and the responsible article don’t distort the science, I do think the conclusion that they draw is not the only one consistent with the data.

Let’s start with the bird that is being discussed. It’s the Aldabra white-throated rail, whose scientific name is Dryolimnas [cuvieri] aldabranus. It lives on the Aldabra atoll in the Indian Ocean and is nearly identical to white-throated rails (Dryolimnas cuvieri) found in other parts of the world, like Madagascar. However, the ones on the Aldabra atoll cannot fly, while the others can. As a result, the flightless birds on the atoll are considered a subspecies of the version that can fly.

While we cannot say for sure, the generally-accepted origin story for the Aldabra white-throated rail is that normal white-throated rails landed on the atoll, and since there were no predators there, they stayed. Since they didn’t need to fly anymore, they evolved into flightless birds over several generations. This makes sense, because when a population of organisms doesn’t need a particular biological trait, mutations can degrade those traits without affecting survivability. In addition, DNA is so incredibly well-designed that over the course of generations, it can “turn off” genes that are no longer used in order to save energy. As a result, it makes sense that these flightless birds are descendants from birds that could originally fly.

Why do these articles discuss the birds being extinct at one point? Because the authors of the scientific study looked at the fossil record of the atoll. Using scientifically-irresponisble dating methods, they came to the conclusion that the atoll was completely underwater about 140,000 years ago. When they looked at fossils they interpreted to be older than 140,000 years, they found two bones that seem identical to the corresponding bones in the Aldabra white-throated rails that currently live on the atoll. Thus, they conclude that these flightless birds lived on the atoll before it went completely underwater.

Well, since the birds couldn’t fly, the authors assume that they all died when the atoll was underwater. However, in fossils that they interpret as being deposited after ocean levels decreased and the atoll was no longer underwater, they found another bone that looks similar to the corresponding bones in white-throated rails that can fly. However, it is heavier and more robust than what is found in those birds, but still lighter than what is found in the flightless Aldabra white-throated rails. In other words, it seems to be “in between” the bone of a normal white-throated rail and a flightless white-throated rail. To them, that gives “irrefutable evidence” (their words) that the Aldabra white-throated rails evolved twice: once before the atoll went underwater, and once after.

While their interpretation of the evidence makes sense and is consistent with all the known data, their case is certainly not “irrefutable.” First, you have to assume that they are interpreting the fossil record correctly. There is a lot of evidence to indicate the earth isn’t anywhere close to 140,000 years old, and if that evidence is correct, then their entire explanation is wrong. Also, even if the earth is as old as these scientists want to believe, the authors’ explanation is not the only one consistent with the data. We know that flightless animals can move from place to place on floating mats of vegetation. This is called “rafting,” and it is used by both evolutionists and creationists to explain the worldwide distribution of certain animals. If the atoll flooded like the authors think, the flightless birds could have survived by rafting. What about that one bone that is “in between” the two subspecies? There are natural variations in all bones. A “more robust” bone from a normal white-throated rail can be explained by natural variation within a population of normal white-throated rails.

The main reason I am writing about this is not to argue with the authors. It’s to point out the deceptiveness of articles like the one I quoted at the beginning of the post. As I have said many times before, do not believe the things you read in the popular press when it comes to science. Most “science journalists” are profoundly ill-equipped to understand science, and usually quite poor journalists as well.

A Bacterium That “Eats” Carbon Dioxide…and a Creationist Prediction

A false-color scanning electron microscope image of Escherichia coli. The different colors represent bacteria with different traits.

Escherichia coli (E. coli) are the workhorses of the bacterial world. They are found in every human being and most warm-blooded animals, but they are also found in laboratories all over the world. Because they are easy to care for, reproduce quickly, and have a genome that is reasonably well-understood, they are a popular subject of study among biologists. In addition, they end up producing a lot of chemicals that we need but are unable to produce ourselves. For example, insulin is a protein that all people need, but some people don’t make enough of it (or don’t respond well enough to it) to remain healthy. That leads to diabetes, and one treatment for diabetes is regular insulin injections.

While the insulin in pigs and cattle is close to what we find in people (and was used to treat diabetes for a long time), the best insulin for most diabetics is human insulin. Unfortunately, even with the best technology available, we aren’t good enough chemists to make insulin, but simple organisms like bacteria are. As a result, scientists have learned how to insert the human gene for insulin into a bacterium, which allows the bacterium to do the chemistry for us. As a result, much of the insulin used to treat diabetics today is human insulin produced by E. coli bacteria.

Unlike some species of bacteria, however, E. coli have to eat in order to get the energy and raw materials they need to do that chemistry. This ends up producing carbon dioxide as waste. To reduce the buildup of carbon dioxide in the atmosphere, then, it would be nice to produce chemicals like insulin from an organism that does not produce carbon dioxide in order to live. There are technical problems with that, however, so right now, diabetic insulin (and many other medically-related chemicals) adds to humanity’s “carbon footprint.” There are two ways to fix this: Either figure out how to use organisms that don’t have to eat (like organisms that make their own food through photosynthesis) or change E. coli so that it doesn’t have to eat.

In a recent study, scientists have been working on the second alternative and have experienced some success. As a byproduct, they have produced something that can be used to test creationism.

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Another High-Profile Defection from Darwinism

Yale computer science professor Dr. David Gelernter (click for source)

The High Priests of Science continue to assure us that there is no debate when it comes to the validity of evolution as an explanation for the history of life. As the National Academy of Sciences says:

…there is no debate within the scientific community over whether evolution occurred, and there is no evidence that evolution has not occurred. Some of the details of how evolution occurs are still being investigated. But scientists continue to debate only the particular mechanisms that result in evolution, not the overall accuracy of evolution as the explanation of life’s history.

The problem, of course, is that such dogmatic statements are not consistent with the data that is supposed to guide scientific inquiry. When people honestly evaluate such data, many see how wrong the High Priests of Science are. Nearly two years ago, for example, I wrote about a world-renowned paleontologist who put up a display in his museum showing how there was no controversy about evolution. The problem, of course, is that he had never investigated all the data. When he got up the courage to actually read books written by scientists who point out the many flaws in evolutionary thinking, he ended up being convinced by the data and defected away from Darwinism. This cost him his job, but at least his scientific integrity remained intact.

Now there is another addition to the list of high-profile academics who had the courage to investigate all the data. His name is Dr. David Gelernter, and he is a professor of computer science at Yale University. In May of this year, he wrote a very interesting article for The Claremont Institute. I encourage you to read the article in its entirety, but I cannot help but add a bit of “color commentary.”

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Soft Tissue Showdown

Soft tissue structures in a dinosaur bone that the authors interpret as biofilms left by modern bacteria (image from study being discussed)

Since Dr. Mary Schweitzer shocked the paleontological community with her discovery of what appears to be soft tissue in a dinosaur fossil, scientists rushed to find more examples of such soft tissue in fossils that are thought to be many millions of years old. They were apparently successful (see here, here, here, here, and here, and here).

Reactions to these finds follow one of three schools of thought. Some in the scientific community (like myself) beleive that the soft tissue is from the creatures that made the fossils and is therefore evidence that the fossils are not millions of years old, since there is no plausible mechanism by which soft tissue can stay soft that long. Some believe that the soft tissue is from the creatures that made the fossils and are seeking a means by which it could stay soft for millions of years. So far, those attempts have not been successful (see here, here, and here). The rest accept the seemingly obvious fact that soft tissue cannot possibly stay soft for millions of years and therefore argue that the soft tissue that has been found cannot be from the creatures that made the fossils. The results of a recent study at least partially support the view of those in the third camp.

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A Frustrating Book, But A Good First Step

A new, honest book about the creation/evolution controversy with the church.
When the creation/evolution controversy comes up in Christian circles, it is often accompanied by a lot of strife. Some Christians think that evolution comes straight from the Devil, while others think that when Christians refuse to accept the fact of evolution, they are harming the cause of Christ. Unfortunately, most of the major Christian organizations that focus on the subject fuel this acrimony. As a result, when I heard that the Colossian Forum had convinced Dr. Todd Wood (a young-earth creationist) and Dr. Darrel R. Falk (a theistic evolutionist) to write a book about the subject, I was intrigued. I actually pre-ordered a copy of the Kindle version, but later was happy to find that the publisher had sent me a free paperback copy to review.

The book, entitled The Fool and the Heretic, is made up of chapters written by Dr. Wood (the “fool”), chapters written by Dr. Falk (the “heretic”), and short interludes written by Rob Barrett of the Colossian Forum. There are also discussion questions at the end of each chapter. Drs. Wood and Falk are diametrically opposed when it comes to the question of origins, and that becomes clear right up front. Indeed, the first chapter (written by Wood) is entitled “Why Darrel is Wrong and Why It Matters,” and the next chapter (written by Falk) is “Why Todd is Wrong and Why It Matters.” Because of those titles, I almost named this review, “Why Todd, Darrel, and Rob are all wrong and why it matters,” because that’s the main conclusion I was left with when I finished the book.

Both initial chapters present the standard view from each camp. Dr. Wood says that Dr. Falk is wrong because when you try to interpret the first eleven chapters of Genesis to be anything other than historical narrative, you end up doing great theological damage to the rest of the Bible. Dr. Falk says that Dr. Wood is wrong because the evidence for evolution is overwhelming, and when Christians reject that evidence in order to hang on to an outdated view of Scripture, it ends up causing great damage, especially to those who are interested in pursuing the truth. They will eventually encounter this overwhelming evidence, and it will produce a crisis of faith, which sometimes results in leaving the faith. Of course, neither of those assertions is new, and in my view, neither of them is correct.

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No, These Researchers Did Not See a Single-Celled Organism Evolve Into A Multicellular Organism!

A green algae in a predator-free environment (far left) and other environments with predators. (click for credit)

A student sent me an article from Science Alert, asking me about its rather bold claim:

Scientists Have Witnessed a Single-Celled Algae Evolve Into a Multicellular Organism…Most of us know that at some point in our evolutionary history around 600 million years ago, single-celled organisms evolved into more complex multicellular life. But knowing that happened and actually seeing it happen in real-time in front of you is an entirely different matter altogether. And that’s exactly what researchers from the George Institute of Technology and University of Montana have witnessed – and captured in the breathtaking, time-lapse footage below.

Over the course of my scientific career, I have learned that many science journalists are terrible at science and not much better at journalism, so I did what I always do when I read about science in the popular press: I found the scientific article upon which it was based. Not surprisingly, the study didn’t do what the article claims. It did find one interesting result, however.

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Big News in Epigenetics!

The Grand Prismatic Spring in Yellowstone National Park holds bacteria like the ones in the study being discussed.
(click for credit)

The more we learn about creation, the more it surprises us. While it is true in all areas of science, it seems particularly true in genetics. When I was at university, I was taught as definitive fact that each gene in my DNA determined the makeup of one protein in my body. We now know that is false. I was also taught as definitive fact that the only way a parent can transmit a trait to its offspring is through the sequence of nucleotide bases in DNA. As a result, if a new trait appears in a population, it must be due to a change in the species’ DNA sequence. We now know that is false. For example, I was taught as definitive fact in university that cave fish are blind because of mutations to their DNA. We now know that is false, at least for one species of blind cave fish.

So we now know that there are ways to inherit traits that go beyond the DNA sequence that you inherit from both parents. For example, we know that if you train mice to fear a certain smell, the next generation can inherit that fear. It’s not that the parents train the fear into their offspring (the offspring were raised separate from their trained parent). They actually inherited the fear. How in the world can a parent pass on a fear of something to its offspring? That’s what the field of epigenetics (which literally means “on top of genetics”) wants to find out.

We know that it has something to do with how an organism regulates the activity of its genes. An organism can alter chemical aspects of the DNA that are not related to its actual sequence, and that alteration can decrease the use of a gene, increase the use of a gene, turn a gene off so that it is not used at all, or turn a gene on so that it will start being used. For example, most people are not born lactose intolerant. After all, they drink their mother’s milk or a milk-based formula. Milk digestion requires the enzyme called “lactase,” which is coded for by a gene. While everyone has that gene turned on at birth, in some people, it gets turned off later on, causing lactose intolerance. Nothing has changed in the person’s DNA sequence – the gene is still there and has not been broken. However, that gene has been turned off by epigenetic mechanisms. It is thought that this process is responsible for epigenetic inheritance. To some extent, we must be able to inherit the “off” and “on” status of our parents’ genes.

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Another Failed Evolutionary Prediction

A common fruit fly, Drosophila melanogaster (click for credit)

The acid test of a scientific theory is whether or not it can make testable predictions about things that are not known. If it can’t, it isn’t really a scientific theory. If it can, those predictions should be tested by observation or experiment. If the results of the test confirm the predictions, you can have more faith in the theory. If they do not, you must either alter your theory or abandon it. One of the main reasons I am a creationist is that creationism has made many testable predictions, and many of those predictions have been confirmed. In fact, creationism has a much better track record when it comes to confirmed predictions than does evolution (see here and here).

Recently, I ran across another study that demonstrates another failed prediction of evolutionary theory. It studied the alcohol dehydrogenase protein (ADH) as made by fruit flies. Fruit flies often consume alcohol because they feed on rotting materials, and the ADH they make allows them to do that. How do they make ADH? They have a gene that gives the necessary instructions to the cell. That gene is, in effect, a “recipe” for ADH.

Studies have already shown that the common fruit fly (Drosophila melanogaster) tends to feed on alcohol-rich things (like rotting fruit) more than a similar fruit fly, Drosophila simulans. The evolutionary explanation that has always been given for this fact is that these two fruit flies had a common ancestor, and that ancestor had a gene that made less efficient ADH. As a result, the common ancestor didn’t eat alcohol-rich things.

The evolutionary line that led to the common fruit fly experienced mutations in the ADH gene, and those mutations ended up making the ADH more efficient. Natural selection then caused those fruit flies to survive, because they could now survive by eating a lot of rotting fruit, while the other flies could eat only a little rotting fruit. That process continued over time, eventually leading to the common fruit fly we see today, which eats a lot of rotting fruit. In evolutionary biology lingo, we would say that the common fruit fly underwent “positive selection” in its ADH gene, while the other fruit fly did not.

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Directed Evolution Wins Nobel Prize

From left to right: Dr. Frances Arnold, Sir Gregory Winter, Dr. George Smith
(Credits:Beavercheme2, Aga Machaj, Univ. Missouri-Columbia)

Yesterday, the Royal Swedish Academy of Sciences announced that the Nobel Prize in chemistry will be shared among three scientists who all used directed evolution to engineer proteins that solve problems. A reader who saw a news story about the announcement asked me to explain what “directed evolution” means, and I am happy to oblige. In directed evolution, scientists use the concepts of variation and selection to take a molecule that already exists in nature and adapt it to do something that they want it to do. Using a concrete example that comes from the research of Dr. Frances Arnold (one of the recipients) is probably the best way to explain the process.

Dr. Arnold’s lab started with a naturally-occurring enzyme charmingly named P450 BM3. Enzymes speed up specific chemical reactions, and P450 BM3 speeds up the reaction in which an oxygen atom is inserted between a carbon atom and a hydrogen atom in a fatty acid molecule. This is an important step in the process by which a living organism breaks down fatty acid molecules. Dr. Arnold’s lab was interested in doing the same kind of reaction, but on a different type of organic molecule: a small alkane. The enzyme P450 BM3 couldn’t initially do that. However, it could weakly speed up that reaction on large alkanes.

Since the enzyme could at least do that, Dr. Arnold thought that she could “tweak” it until it did exactly what she wanted it to do. However, enzymes are absurdly complicated molecules, and human science isn’t very good at making or understanding them. So she decided to let better organic chemists (bacteria) do the heavy lifting. Her lab took the gene that tells bacteria how to make P450 BM3 and subjected it to mutations. They then saw whether or not the resulting enzyme made by bacteria was any closer to being able to do what they wanted it to do. Maybe it did a better job speeding up the reaction on a large alkane, or maybe it was able to speed up the reaction on a shorter alkane. If that was the case, they saved that gene and allowed it to mutate more, seeing if any more progress could be made. If not, they threw it away and tried again.

This is why the process is called “directed evolution.” Dr. Arnold’s lab induced mutations (which are a source of genetic change in organisms) and then selected any enzyme that ended up being better at what they wanted it to do. With enough of those steps, they were able to get what they wanted: an enzyme that inserted an oxygen atom between a carbon atom and a hydrogen atom in a small alkane. In the end, the process had changed just over 2% of the molecule, but that was enough to change it from an enzyme that acted on fatty acids to one that acted on small alkanes.

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