Ancient DNA: Too Good to Be True?

The search for ancient DNA has captivated scientists and the public alike for decades. The possibility of uncovering genetic information from long-extinct species promises to revolutionize our understanding of evolution and prehistoric life and makes one wonder if Jurassic Park might be possible However, the field of ancient DNA research has been fraught with controversies, false starts, and methodological challenges.

I recently was sent a manuscript that made some extraordinary claims about extracting DNA from Early Cretaceous fossils. In this blog post, I will summarize some of my analysis of these claims, why they are likely too good to be true and what this tells us about the current state of ancient DNA research. For a more detailed breakdown, check out my full video analysis here:

The Paper’s Extraordinary Claims

The paper in question, titled “Insights from Early Cretaceous: The Promise of Lopa Ancient DNA Sequencing,” appeared on a preprint server for biology about a year ago.  You can read it here: https://www.biorxiv.org/content/10.1101/2023.06.18.545504v1.article-metrics  Its authors claim to have successfully extracted and sequenced DNA from fossilized fish dating back to the Early Cretaceous period, approximately 120-140 million years ago. If true, this would be a groundbreaking discovery, pushing back the timeline for recoverable DNA by over 100 million years!

Some of the paper’s key claims include:

1. Extraction of DNA fragments up to 300 base pairs in length from Cretaceous rock samples
2. Identification of DNA sequences from not just the fossilized fish, but also their parasites and prey
3. Recovery of over 11 million DNA sequence reads from a single rock sample

These claims are truly astounding – and that’s precisely why they warrant careful scrutiny.

Red Flags in Methodology

As I began to read the paper’s methods section, several red flags emerged. Here are a few of them.

Questionable Sample Preparation:  The authors describe washing the rock sample with tap water and a DNA cleaner solution. They then cut and ground the sample into a powder. There’s no mention of working in a clean room or taking precautions against modern contamination.

This approach is a far cry from the ultra-sterile techniques used in reputable ancient DNA labs. The lack of contamination controls is particularly concerning given the extreme age of the purported samples.

Implausible DNA Quality: The authors report recovering DNA fragments with an average length of 139 base pairs. This is remarkably long for DNA that’s supposedly 120+ million years old. For comparison, DNA from much younger samples (like Neanderthals or woolly mammoths) typically yields fragments averaging 40-50 base pairs.

Contamination Concerns: Perhaps the most glaring issue is the vast array of DNA sequences the authors claim to have recovered. Their list includes modern crop plants (wheat, corn, rice), domesticated animals (chickens, pigs, cattle), a lot of human sequences, viruses and many more.

While the authors acknowledge that some of these are likely contaminants, they still claim to be able to differentiate between “ancient” and modern DNA sequences. However, they don’t provide a clear explanation of how they made this distinction.

The Importance of Skepticism in Science

As exciting as the prospect of Cretaceous DNA might be, it’s crucial to approach such extraordinary claims with a healthy dose of skepticism. There are several reasons why the scientific community is likely to be dubious of these results:

1. Historical Context: In the late 1990s and early 2000s, there were several high-profile claims of extremely ancient DNA that were later debunked. These incidents led to the development of rigorous protocols for ancient DNA research, which this paper doesn’t seem to follow.
2. Lack of Damage Patterns: Truly ancient DNA should show characteristic patterns of damage, particularly in the ratios of certain bases. The authors don’t provide clear data on these damage patterns, which is a standard practice in ancient DNA studies.
3. Implausible Preservation: While it’s theoretically possible for some DNA to survive for millions of years under extraordinary conditions, the quality and quantity of DNA reported in this paper stretch the bounds of credibility.
4. Absence of Peer Review: The fact that this paper has remained on a preprint server for over a year without progressing to publication in a peer-reviewed journal is telling. It suggests that the work may not have passed muster with expert reviewers.

Lessons for Science Communication

This paper and its extraordinary claims offer some valuable lessons about science communication and the importance of critical thinking:

1. Preprint Caution: While preprint servers serve a valuable role in rapidly disseminating scientific findings, it’s crucial to remember that these papers haven’t undergone peer review. Extraordinary claims require extraordinary evidence – and scrutiny.
2. Methodological Rigor: In fields like ancient DNA research, where contamination is a constant concern, adherence to established protocols is paramount. Any departures from these protocols should be clearly justified and validated.
3. Contextual Understanding: It’s important to consider new findings in the context of established knowledge. Claims that dramatically push back the boundaries of what we thought possible should be met with particular scrutiny.
4. Interdisciplinary Approach: Evaluating complex scientific claims often requires expertise from multiple fields. In this case, understanding the paper requires knowledge of molecular biology, paleontology, and the specific challenges of ancient DNA research.

Reflections on Ancient DNA Research

While I’m skeptical of the claims made in this particular paper, I remain excited about the future of ancient DNA research. Legitimate studies continue to push back the boundaries of recoverable DNA, providing invaluable insights into extinct species and ancient ecosystems. However, progress in this field is likely to be incremental rather than revolutionary.

As we continue to explore the genetic echoes of the distant past, it’s crucial that we maintain high standards of evidence and remain open to both the possibilities and limitations of our methods. The story of ancient DNA research is far from over – but separating fact from fiction will require rigorous science, critical thinking, and a healthy dose of skepticism.