Challenges to Conventional Scientific Views on DNA and Soft-Tissue Preservation in Fossils

After releasing my YouTube video critiquing a Young Earth Creationist (YEC) interview on dinosaur fossil soft tissue preservation, I received a thoughtful email from one of the interviewees. They kindly offered to clear up what they saw as misunderstandings in my critique and presented several challenges to the conventional scientific view on fossil preservation that they believed I might be unaware of or should reconsider again.

First, I want to thank this viewer for reaching out. Their willingness to engage in further discussion is commendable, and I’m happy to have this opportunity to be challenged and thus provided the opportunity to reflect more on this topic. 

In their email, this individual raised several interesting points about Mary Schweitzer’s famous work on soft tissue preservation, the staining of ancient DNA in dinosaur cells, informed me of  some recent manuscripts on DNA preservation in the fossil record which I had not heard about and challenged me on ancient artwork depicting dragon-like creatures. As I began to write some responses I thought it might be worth working my responses into a blog-type post that I could share with my readers which is what you are reading now.

What you will find below are the questions and challenges (in italics) that were addressed to me and my responses. My responses are by no means comprehensive, but they provide my thoughts derived from my general and sometimes very specific knowledge of the ancient DNA/soft-tissue preservation literature.

Ok, let’s get started:

Response to Young-Earth Creationist Questions on Dinosaur Soft Tissue

Thank you for sharing your thoughts and questions regarding the preservation of soft tissues in dinosaur fossils. I appreciate the opportunity to address these points and hope to provide information that reflects the current scientific understanding of this still developing field of study. I find these fossils really fascinating and have had an opportunity to talk with several scientists who are engaged in paleontological research in this area. It’s a growing field of study, as you know, with many questions that remain unresolved.  I will try to provide some perspective on your questions and comments from my knowledge in this area.

1. Mary Schweitzer’s Hemoglobin Iron Experiment

Mary Schweitzer’s hemoglobin iron experiment preserved tissues in the lab for only a few years. This is very different from fossil conditions over millions of years. Demonstrating it preserves tissue over a few years is just not convincing enough for me to extrapolate to millions of years. 

While I understand your skepticism about extrapolating Schweitzer’s short-term experiment to millions of years, it’s important to consider several key points:

1. Schweitzer’s experiment was not intended to directly replicate millions of years of preservation. Rather, it demonstrated a potential mechanism that could contribute to long-term preservation. The iron in hemoglobin was found to act as a preservative, slowing down decay processes significantly [1]. This discovery opened up new avenues for research into how soft tissues might be preserved over very long time periods. It’s important to note that scientists don’t simply extrapolate from short-term lab experiments to millions of years. Instead, they use these experiments to identify potential mechanisms and then look for evidence of these mechanisms in actual fossil samples. Other factors that contribute to exceptional preservation include rapid burial, low oxygen environments, and mineralization processes [2].

2. The conditions within tiny pores of dinosaur bones differ greatly from typical laboratory settings. Factors like mineral association, limited oxygen exposure, and cross-linking of proteins can dramatically increase preservation potential.
3. We have numerous examples of biomolecule preservation over millions of years in other contexts, such as residue of amino acids in fossil shells. This shows that under the right conditions, organic materials can persist for extremely long periods.
4. The rate of soft tissue decomposition varies enormously depending on environmental conditions. For example, the Tollund Man’s skin was preserved for over 2,000 years in bog conditions – a preservation rate over 25,000 times slower than typical decomposition.
5. Multiple independent lines of evidence, including radiometric dating of surrounding rock layers, consistently point to these fossils being millions of years old. The soft tissue preservation, while surprising, does not negate this other evidence.

While more research is needed to fully understand the mechanisms at play, the current evidence suggests that some forms of soft tissue preservation over millions of years is possible under specific conditions. It’s important to consider all available evidence rather than dismissing findings based on initial skepticism. The discovery of preserved soft tissues has led to a reevaluation of fossilization processes, which has thus far not led to reasons to doubt the fundamental principles of geology and paleontology that support an ancient Earth.

2. Dinosaur Soft Tissue Findings

Dino blood cells, blood vessels, bone cells, and cartilage cells have all been thoroughly documented in the scientific literature. You mentioned no blood cells. 

I apologize for any confusion, but I need to clarify some important points regarding the findings of blood cells and other soft tissues in dinosaur fossils:

1. While structures resembling blood vessels, bone cells, and cartilage have indeed been found in some dinosaur fossils, actual blood cells have not been conclusively identified. The round, red structures initially thought to be blood cells were later determined to be iron-rich nanoparticles, likely formed through geochemical processes.
2. Mary Schweitzer, a key researcher in this field who I have spoken to personally about this very question, has stated that what’s been found are not intact cells as we would find in living organisms. Rather, they are typically mineralized structures that have retained the shape of original cells and may contain the degraded highly-modified remnants of cellular components [3].
3. When paleontologists refer to “soft tissues” in fossils, they’re often talking about preserved organic structures or biomolecules, not necessarily intact cells or tissues as we would find in modern organisms. The term “soft tissue” in paleontology can refer to a range of preserved organic materials, from actual tissue remnants to mineralized impressions of original tissues [4].
4. While traces of proteins and even fragments of DNA have been detected, these are not fully intact molecules analogous to modern molecules but highly degraded remnants. There are particular classes of biomolecules that are more resistant to degradation or become modified reaching incredibly stable states (e.g. porphyrins as the breakdown product of hemoglobin and also found in crude oil).

It’s crucial to understand that the presence of these preserved structures doesn’t contradict the fossil’s great age. The preservation of these structures similar to living cells and modified remains of original biomolecules is indeed remarkable and has provided valuable insights into dinosaur biology. However, their presence doesn’t necessarily indicate that the fossils are only thousands of years old. Instead, it has led scientists to reevaluate the processes of fossilization and to investigate mechanisms that could allow for such preservation over millions of years [5, 6, 7].

I should reiterate I know of no fossils dated to more than 1 million years old that have preserved blood cells. This is why I said that no blood cells have been found. Yes, evidence that blood cells were once present at that location, or the forms of blood cells have been preserved but not most of the original biomolecules which have been replaced.

It’s also worth noting that the quality and extent of soft tissue preservation can vary greatly between fossils, depending on the specific conditions of burial and fossilization. Not all dinosaur fossils contain preserved soft tissues, and those that do often show varying degrees of degradation consistent with their great age [8].

I slightly out-of-date article but a must read on biomolecule preservation and the misunderstandings that some creationists have about those molecules is found a the Letters to Creationists blog (https://letterstocreationists.wordpress.com/dinosaur-soft-tissue/)  

3. Ancient DNA (aDNA) Staining in Dinosaur Cells

Prominent paleobiologists from the Chinese Academy of Sciences and Mary Schweitzer’s research group have confirmed the aDNA stain is from the dino cell nuclei (bone and cartilage cells). It is not DNA outside the nuclei from bacteria etc. It stains identically to extant bird cells. 

I agree, the staining of cell nuclei in dinosaur fossils is an exciting area of research. You’re correct that researchers, including Mary Schweitzer’s group and scientists from the Chinese Academy of Sciences, have reported positive results from these staining techniques [8]. However, it’s important to understand the limitations and interpretations of these findings.  The Baillul et al articles [6 and 7] is especially interesting and the location, chondrocytes within bone lacunae, of where preservation of soft tissues signatures is found is consistent with extremely rare conditions of good preservation and to me is not all that surprising.

When scientists observe positive staining for aDNA (ancient DNA) in fossil samples, it indicates the presence of organic compounds that react similarly to DNA with these stains. While this is suggestive of preserved DNA, it’s not definitive proof of intact and in particular, readable genetic material [9].

The similarity in staining between dinosaur cells and extant bird cells is indeed intriguing and supports the evolutionary relationship between dinosaurs and birds. However, this similarity doesn’t necessarily indicate that the dinosaur DNA is as well-preserved as modern DNA. The staining techniques are sensitive but can’t distinguish between highly fragmented DNA or highly modified DNA preserved by crosslinking with other molecules and intact DNA. Much more research needs to be done on the limits of this form of staining to make any definitive statements [9].

Once again it’s also crucial to note that while these staining techniques are valuable tools, they are just one part of a larger body of evidence. Scientists use multiple methods to study ancient biomolecules, including advanced sequencing techniques and mass spectrometry [10 and 11] and more and more tools are being brought to bear on these fossils each day. I expect we will learn much more in the next few years.

4. DNA Degradation and Time

The amount of stained DNA in the woolly mammoth and dinosaur was about a 3 micrometer diameter. I was referring to the amount being so similar despite the drastic time differences between them (from a Darwinistic) perspective. There should be much less DNA than in a woolly mammoth if they are separated by millions of years because it would have degraded. Also, the amount of stained DNA between the dino cells and the extant bird and reptile cells was not that much different to justify millions of years. Maybe thousands, but not millions. 

Your observation about the similarity in stained DNA amount between woolly mammoths and dinosaurs despite their vast age difference is an interesting point. However, it’s important to understand that the amount of stainable material doesn’t directly correlate with the amount of intact, readable DNA. The quality is of question and we also don’t know what other breakdown parts of other organic molecules in fossils may trigger similar staining patterns. Again, this is fairly preliminary research and so one shouldn’t seek to reach definitive conclusions at this point.

DNA degradation is indeed a time-dependent process, but it’s also heavily influenced by environmental factors such as temperature, pH, and the presence of microorganisms. In some exceptional preservation conditions, small amounts of very ancient DNA can persist, although typically in a highly fragmented state. I expect that like portions of collagen fibers, porphyrins and melanosomes molecules there could be other molecules including DNA that could experience chemical modifications that result in their being left in an ultra-stable state that could persist for many hundreds of millions of years.

The similarity in staining between dinosaur cells and modern bird or reptile cells doesn’t necessarily imply that the quality or quantity of DNA is the same. The staining process can react with degraded DNA fragments or other biomolecules that persist in the fossil, giving a similar appearance to intact DNA in modern cells [9].

It’s also worth noting that our ability to detect and analyze ancient DNA has improved dramatically in recent years. Scientists have successfully sequenced DNA from specimens hundreds of thousands of years old, and in exceptional cases, even older [12]. However, retrieving readable DNA sequences from dinosaur fossils has thus far remained elusive. Even replication of Mary Schweitzer’s work I have not seen successfully done. This certainly points to dinosaur remains being significantly older than those of mastodons, mammoths and other Ice Age fauna which in a Young-earth model of earth’s history are not significantly different in age.

5. Quality of Dinosaur Cell Preservation

The quality of dinosaur cells is very close to those of extant birds and reptile cells. I have Mary Schwitzer’s microscope images and those from the Chinese Academy of Sciences. 

The microscope images showing well-preserved dinosaur cell structures are really amazing. However, it’s important to interpret these images in the context of fossilization processes.

What we’re seeing in these images are typically mineralized replicas of the original cell structures, not the actual original biomolecules in their original condition as they existed in the living dinosaur. Over millions of years, the original organic material is typically replaced by minerals, preserving the shape and sometimes even subcellular details of the original cells.  Now, as I noted earlier, some of these fossils do contain original biomolecules but they have undergone extreme modification even while remaining in the positions they were in the original cell. Visual appearance of similarity in size and shape is not the same as their being the same just as two bacteria that look similar under a microscope don’t mean they might not be in different domains (eubacteria vs archaebacteria) or looking at a picture of a flying squirrel and a sugar glider and coming to the conclusion they are just variation of the same kind of organism. 

The similarity between these fossilized structures and modern cells is a witness to the effectiveness of the fossilization process in preserving morphological details. However, this similarity in appearance doesn’t necessarily indicate that the biochemical composition of these structures is the same as in modern cells.

If these “soft tissues” and reports of preserved cells such as blood cells were actually similar to today’s cells it would not be difficult to confirm. Blood cells and all other cells are bound by a plasma membrane. The presence of such a membrane should be easily confirmed by relatively simple chemical analyses. And yet no reports are found in the literature. These would be easy to do by young-age creationist and yet they have not shown the presence of many basic cellular macromolecules present in all cells. The appearance of a cellular shape then is not due to preservation of the cell but must come from replacement of molecules of the cell or material accreting around the cell prior to its degradation leaving the shapes of cells visible but not the cells themselves.

6. Increasing Reports of Biomolecule Preservation in Fossils

There are many papers in the scientific literature documenting well preserved biomolecules from fossils. Attached is a list of some of these papers. But, the list has grown!

The list is most definitely growing, and I would expect it to continue to grow at an accelerating pace. However, that list cultivated by Brian Thomas at the Institute for Creation Research is not well curated. He seems to include every report with no discernment as to the veracity of the report. For example, he lists multiple papers reporting DNA and other biomolecules that were published prior to 1995. None of those are accepted by anyone that I know of in the scientific community today. They are all acknowledged to be the result of sequence contamination. In those years scientists were not as aware of just how easily modern contamination can occur and journals were interested in the surprising and exciting new discoveries.  In fact, the erroneous results and bad reputation that ancient DNA researchers and journals gained in the mid-90s probably set back ancient DNA studies several years. It wasn’t until rigid protocols were established that the field of study started to take off. These older reports should not be listed by Thomas as evidence (he liked to tout the number of reports) of ancient DNA. I’m sure he is aware of this but continues to include them on this list.

However, it’s important to note that the preservation of biomolecules doesn’t contradict the conventional understanding of geological time. Instead, as I’ve pointed out several times, it has led to new research into the mechanisms of exceptional preservation which has added new insights into that preservation process.

The quality and extent of biomolecule preservation can vary greatly depending on the fossilization conditions. In most cases, what’s preserved are highly degraded fragments or altered versions of the original biomolecules, not intact, functional molecules as would be found in living organisms.

7. Ancient DNA Extraction from Cretaceous Fish Fossil

Ancient DNA has been extracted from an early Cretaceous fish fossil from China. Attached is the paper from the prominent lab that produced Nobel prize winners. They did the work and wrote it up. Very interesting that they decided not to get it peer reviewed and officially published. They had enough aDNA to form evolutionary inferences about the fish. Regardless, people are downloading and reading it. This makes me think secular scientists are tiptoeing around sequencing a Cretaceous fossil because it will produce a lot of controversy in science.  

The unpublished work [13] (https://www.biorxiv.org/content/10.1101/2023.06.18.545504v1) you mentioned on aDNA extraction from a Cretaceous fish fossil is intriguing. However, it’s important to approach unpublished results with caution. The peer review process plays a crucial role in validating scientific findings and methodology.

The fact that the researchers chose not to pursue peer-reviewed publication could be due to various reasons, including difficulties in replicating results or concerns about potential contamination. In the field of ancient DNA research, contamination with modern DNA is a significant challenge, especially for very old samples [14 and 15]. Documentation of the exact location and evidence of its age would be critical as well as many reports have been made by YECs of objects found in ancient rocks (for example The London Hammer – see my recent video https://youtu.be/QGwMhpiHwOs?si=gizPZCXD8p8AGqfK) that are not in fact original to those rock layers.

I made a video in which I read portions of this paper and conclude that their case that they have discovered DNA from these fish fossils is very unlikely. The authors definitely did not take the steps necessary to persuade the scientific community that their results are not contamination with modern DNA.

I personally would not be all that surprised to find some evidence of biomolecules that old though I would expect they would be found to be in highly modified forms as thus far has been found. If unmodified proteins had been found with say the original sulfide bonds still in intact. I would find that quite surprising.

8. Artistic Depictions of Dinosaurs in Ancient and Medieval Art

Please purchase the book Dire Dragons, which documents a great deal of the global artwork depicting dinosaurs from the ancient and medieval times. It does not include all the art known. The artistic depictions in tapestry, paintings, sculptures, stone work etc. are very similar to the illustrations created by modern day paleontologists derived from putting together dinosaur fossil skeletons. This was so powerful and convincing for the young age of the dinosaurs. The artworks depicting dragon-like creatures in ancient and medieval times are fascinating from a cultural and historical perspective. However, interpreting these as direct depictions of living dinosaurs requires caution.

Many cultures have myths and legends about dragon-like creatures, which could be inspired by a variety of sources, including discovered fossils, exaggerated tales of living reptiles, or purely imaginative creations [16]. I’ve written about this a few times on this blog (for example, see: https://thenaturalhistorian.com/2023/01/25/dinosaurs-dragons-and-ken-ham-the-literal-reality-of-mythological-creatures-3/).

While some ancient artworks may bear resemblances to modern depictions of dinosaurs, this similarity alone isn’t sufficient evidence that the artists had seen living dinosaurs. Cultural transmission of ideas, fossil discoveries, and coincidental similarities must all be considered as potential explanations [17].

Parenthetically, I would point out that there are plenty of ancient depictions of things that look like spaceships and alien-like creatures. Those that believe we have been visited by extraterrestrials point to these items as evidence of their belief. I don’t find those any more compelling than images that have the appearance of a type of dinosaur. 

Your response raises an intriguing point about ancient artwork potentially depicting dinosaurs. However, interpreting these artworks as evidence for young-earth creationism requires careful consideration of several factors:

1. Cultural context: Many cultures have myths and legends about dragon-like creatures, which could be inspired by various sources, including discovered fossils, exaggerated tales of living reptiles, or purely imaginative creations [16]. It’s crucial to understand the cultural and historical context of these artworks before drawing conclusions.
2. Fossil influence: The discovery of large fossilized bones has been documented throughout history. It’s possible that some ancient artists based their dragon-like creatures on fossil remains they encountered, rather than living dinosaurs [17].
3. Modern interpretation bias: Our modern knowledge of dinosaurs might lead us to see similarities where they may not have been intended. This is a form of pareidolia, where we tend to interpret vague or ambiguous stimuli as something familiar to our modern understanding [18].
4. Diversity of depictions: Dragon-like creatures in ancient art vary widely across cultures and time periods. If these were based on actual dinosaur sightings, we would expect more consistency in their depictions [18].
5. Lack of corroborating evidence: If dinosaurs existed alongside humans in recent history, we would expect to find more direct evidence, such as dinosaur remains in archaeological sites or more explicit historical records 19].
6. Similar claims in other fields: As you pointed out, similar arguments are made about ancient depictions of “spaceships” or “aliens.” The same critical analysis should be applied to both types of claims [20].

While the artworks in “Dire Dragons” are undoubtedly fascinating, they don’t provide compelling evidence for the coexistence of humans and dinosaurs. Instead, they offer valuable insights into how different cultures have imagined and depicted mythical creatures throughout history. The similarity between some of these depictions and modern paleontological reconstructions is more likely due to the universal human fascination with large, powerful creatures and the influence of fossil discoveries on cultural imaginations.

So much more could be said…

This was a lot more than I thought I would write. I hope this response has provided some helpful context and explanations.

Joel

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