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The Clock Within: Neurospora crassa

April 17, 2026

The Clock Within: Neurospora crassa

What is the science behind the clock?

How did the first person just acknowledge that “Oh it’s 12:00 p.m.”? 

Wouldn’t it surprise you to realize that your body already knows time?

The human body has a natural mechanism to tell the precise time without any measuring device.

Even if a person was kept in complete darkness for many days, they won’t forget the time. They will still experience sleepiness and wakefulness but the cycle will gradually change without any synchronization with sunlight.

This question also aroused curiosity in the minds of researchers, but none could have predicted that bread mold would provide the solution.

In 1959, scientists began studying an orange bread mold by the name of Neurospora crassa.

I even did a test like this myself, leaving bread out for several days just to observe what happened to the mold (seen below).

Somehow, this small organism allowed scientists to understand how living things, including humans, keep track of time using a biological clock.

It did not seem too important at first. But as soon as they took it into their laboratory, it did something rather unusual. They placed the fungus in complete darkness, with no sunlight, not even a single outside signal. The fungus could not tell what time it was. Even then, it still grew in certain patterns (Castro-Longoria et al., 2010). It repeated in a consistent cycle, as though the organism already knew what a day looked like.

This insight changed the perspective on time.

Scientists such as Jay C. Dunlap and Jennifer J. Loros concluded that organisms do not just respond to time but keep an internal clock that runs in cycles (Castro-Longoria et al., 2010). Such a system came to be called a circadian rhythm, meaning “biological rhythm occurring every 24 hours.”

Scientists later discovered that this clock runs through interactions among genes and proteins in a cycle. A vital part of this cycle includes a gene whose job is to create a certain type of protein named FRQ (frequency) (Baker et al., 2011).

When the FRQ protein accumulates in the body, it stops being produced. When this protein degrades, production resumes. Through this process, a continuous cycle is formed, allowing time to be regulated. This is known as a negative feedback loop, where a system turns itself on and off (Baker et al., 2011).

This system is not simple. However, there are other genes, which help the organism to sense light. These are collectively referred to as the “white collar” genes (WC-1 and WC-2). They work together in a cycle and are almost always around 24 hours in duration despite any change in the environment.

Humans function with a similar system.

The human brain has an intricate structure called the Suprachiasmatic Nucleus (SCN), which serves as the timekeeper for the organism, regulating physiological processes like sleep, hormone secretion, and body temperature. Just like in fungi, the circadian rhythm is regulated via protein-gene feedback loop mechanism.

Circadian rhythms have been observed across different organisms, suggesting that the biological mechanism for keeping time is ubiquitous and therefore fundamental for any living thing (Aramayo & Selker, 2013).

This was actually quite simple. Our internal clock had always been around.It was only when Neurospora crassa revealed itself that we realized its existence.

References:

Baker, C.L., Loros, J.J., & Dunlap, J.C. (2011). The circadian clock of Neurospora crassa.
https://pmc.ncbi.nlm.nih.gov/articles/PMC3203324/

Aramayo, R. & Selker, E.U. (2013). Neurospora crassa, a Model System for Epigenetics Research.
https://pmc.ncbi.nlm.nih.gov/articles/PMC3783048/

Case, M.E., Griffith, J., Dong, W., Tigner, I.L., Gaines, K., Jiang, J.C., Jazwinski, S.M., Arnold, J.,  (2005). The aging biological clock in Neurospora crassa.
https://pmc.ncbi.nlm.nih.gov/articles/PMC4228622/

Castro-Longoria, E., Ferry, M., Bartnicki-Garcia, S., Hasty, J., Brody, S. (2010). Circadian rhythms in Neurospora crassa: Dynamics of the clock component frequency visualized using a fluorescent reporter
https://www.sciencedirect.com/science/article/pii/S1087184509002242

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  Timothy Durham was convicted of rape when a test showed his DNA genotype matched the DNA recovered from the crime scene. Eye witnesses testified that Durham was in a different state at the time of the incident, but he wasn’t exonerated from his 3000 year sentence until follow up DNA analysis showed that the preliminary forensic analysis used in the trial was misinterpreted (Thomas et al.). DNA testing serves an invaluable part in our criminal justice system, but it comes with complications and bias that can lead to wrongful convictions and misinformed juries.  

Background:

Forensic genetics aims to identify the origin of a biological sample. It can be traced back to Karl Landsteiner who discovered human ABO blood groups. With blood groups, suspects could be eliminated based on their blood type. For example, if a suspect had type A blood and there was type B blood left at the scene by the perpetrator, the investigators could rule out the suspect. Unfortunately, the reverse didn’t work. If the suspect and perpetrator both had the same blood type, it can’t be concluded that the suspect was guilty. Blood identifiers evolved into 8 distinct categories which improved the ability to eliminate suspects, but could only conclude that (if the system matched) it might be the perpetrator or this person might be related to the perpetrator (Jobling and Gill). The field evolved in the 1980s with the discovery of Minisatellites, lines of repetitive DNA that don’t encode proteins. Minisatellite patterns in DNA create what we know today as the DNA fingerprint, and it has a much higher accuracy rate than previous methods (Augustyn et al.). Around the same time, a breakthrough for victims of sexual assault was discovered. In the case of assault, bodily fluids of both the victim and the assaulter can get mixed. A process called differential lysis was created which could selectively increase the concentration of sperm in a fluid sample thereby allowing for accurate DNA testing (Jobling and Gill). Forensics evolved to use single-locus probe testing after several years because of its ease of interpretation. It looked at specific minisatellites that had high variability between subjects. This was the first DNA-based method to be used in a criminal investigation. Two murder homicides from several years apart were connected using DNA evidence. The evidence was then used to exonerate an innocent man, and the guilty party was found when he tried to evade mandatory DNA testing for all men in the small town. His guilt was then reinforced when the DNA profiles matched, and he gave a confession (Jobling and Gill). Finding DNA at a crime scene doesn’t guarantee that you’ll find a murderer. There are issues with non-pure samples and limited samples that make DNA work difficult, and accreditation of facilities and new techniques and take time (Jobling and Gill).  

Subjectivity of DNA Interpretation:

In a 2009 publication, the National Academy of Science discusses the possibility for subjective influence in lab based forensics. The interpretation bias happens in complex cases where, for example, there could be a mixture of DNA. A study published in 2011 looked specifically at this issue. A gang rape happened in Georgia, and the mixture in DNA from the case was used to prosecute one suspect after another suspect took a plea bargain to testify against him. With DNA mixtures, there are three possible conclusions: suspect excluded, suspect cannot be excluded, and inconclusive. If the suspect is excluded, it means that there’s little to no possibility that his DNA is part of the sample. If the suspect cannot be excluded, it means that there’s a possibility that his DNA is part of the sample. In the trial, the DNA examiners who knew the context of the case concluded that the suspect being prosecuted could not be excluded. The 2011 study gave the DNA evidence from this case and the DNA profiles of the suspects to 17 forensic examiners. These examiners had no context of the case, and they all worked independently. Of the 17, only 1 came to the same conclusion (suspect cannot be excluded) as the examiners who knew the context of the case. Twelve of the 17 concluded that the suspect who was prosecuted and convicted had no relation to the DNA found in the sample. Not only does this show that subjectivity occurs due to the context of the case, but the 17 examiners came up with different findings based on their past experiences meaning that not all DNA analysis is objective. Some organizations like the Scientific Working Group on DNA Analysis Methods say that quantitative statistical evidence should be presented with every categorical conclusion, but the US doesn’t require this (Dror and Hampikian).

False Positives:

There are two categories that cause wrongful identification in a DNA report: coincidental matches and false positives. Coincidental matches are DNA matches between two unrelated people. The probability of these matches is about 1 to 500,000 for white individuals and about 1 to 350,000 for black individuals. This small probability of coincidental matches makes people feel confident in DNA evidence. False positives, on the other hand, are matches between DNA and test DNA that result from issues in the forensics lab. There have been multiple cases of forensics labs accidentally switching victim and suspected rapist DNA which lead to convictions that were later overturned when the lab realized the error. There are also cases of misreading or misunderstanding a sample. In a case from 1993, a man was convicted of rape because someone interpreted a mixed sample of victim and perpetrator DNA as an individual sample. The conviction was again overturned. To prevent false convictions, retesting DNA is allowed, but it’s not an efficient solution. Many people are pushing for statistical information on the probability of false positives, so that the jurors can make accurate judgements based on DNA evidence (Thomas et al.).  

Conclusion:

DNA analysis is a useful tool for the criminal justice system, but subjectivity can be an issue in forensic testing. To combat wrongful convictions, there are organizations like The Innocence Project who use DNA testing to free the innocent, but reformed forensic testing standards should be put in place to prevent subjectivity and to ensure juries are correctly informed during trials. https://www.innocenceproject.org/    

Citation:

Augustyn , Adam, et al. “DNA Finerprinting.” Encyclopedia Britannica , 26 Apr. 2018, www.britannica.com/science/DNA-fingerprinting#ref153186. Dror, Itiel E., and Greg Hampikian. “Subjectivity and Bias in Forensic DNA Mixture Interpretation.” Science & Justice, vol. 51, no. 4, 2011, pp. 204–208., doi:10.1016/j.scijus.2011.08.004. Jobling, Mark A., and Peter Gill. “Encoded Evidence: DNA in Forensic Analysis.” Nature Reviews: Genetics, vol. 5, no. 10, Oct. 2004, pp. 739–751., doi:10.1038/nrg1455. Thompson, William C, et al. “How the Probability of a False Positive Affects the Value of DNA Evidence.” Journal of Forensic Sciences, vol. 48, no. 1, Jan. 2003, pp. 1–8., doi:10.1520/jfs2001171.