The Mind Behind the Brain of a Fruit Fly

Sometime early in the new year, families make their way outdoors to take down the lights they had strung up months before. In their haste to get Christmas back in the box, some of those lights will be wadded into a proverbial tangle of wires which will try their patience come November. It is this kind of tangled mess one might associate with the image recently shared in the media of the brain of a fruit fly, but the fruit fly’s brain is far from a tangled mess.

As reported by the New York Times[1], groups of scientists from the Howard Hughes Medical Institute and Google have been working together since 2014 to map out the architecture of the brain of the fruit fly – what is referred to as a connectome (you can actually see this online – Google it!). The brain of a fruit fly which is about the size of a poppy seed contains about 100,000 neurons. At the time of reporting, the current connectome for the fruit fly has mapped around 25,000 neurons and 20 million synapses! The intent of this research is to hopefully be able to follow the firing of individual neurons and discover how a simpler brain is able to receive and process sensory information.

A population of neurons that is responsible for updating the fly’s internal compass. FlyEM/Janelia Research Campus

At the same time, various teams of scientists around the world[2] are working on determining the gene networks which are responsible for constructing the precise network of neurons and glial cells found in the fruit fly brain. Realize that the building of this precise wiring begins when the larva enters the pupal stage – its brain is essentially destroyed and then reconstructed in a few days before emerging as an adult. So far, scientists have identified genes which regulate cell proliferation in separate regions of the brain, but nothing that would determine the placement of thousands of individual neurons and their millions of necessary synapses.

While the hopeful outcome of these lines of research is primarily to better understand how the brain works, some have expressed the hope that it will give insight into how the brain has evolved[3]. Brains certainly have become more complex over time, but can this increasing complexity be explained by random gene mutations and natural selection alone? I think the complexity found even within the brain of a fruit fly suggests otherwise.

Realize that a fruit fly has no luxury of parental nurturing and a time for formative learning. When the adult fly emerges from its pupal case, its brain must be prewired and ready to execute a large number of complex innate behaviors. After expending tremendous amounts of energy transforming from a worm into an adult fly, you might imagine the first order of business is for that fly to find some food. Consider a sampling of innate behaviors required for this “simple” task:

Fruit flies feeding on a rotten banana
  • There must be a chemosensory receptor on the antennae which will bind to the scent molecules characteristic to rotting fruit (acetic acid). When triggered, these receptors must generate an electrical impulse which is carried by neurons to the fly’s brain.
  • The brain must be able to respond to these electrical impulses. This sense detection must not only indicate the presence of the scent molecule, but the strength of the signal is equally important. Recently, researchers have determined the concentration of this scent molecule must be within a certain range – it cannot be too strong or too weak.[4]
  • The fly must be able to initiate flight which itself defies an evolutionary explanation (see here, here and here). More than just becoming airborne, the fly must be able to control its direction of flight.
  • In flight, the fly must possess an internal sense of orientation (e.g. which way is up, which way is forward, where am I going, where did I come from).
  • In flight, the brain receives further information from sensory hairs on the body and the wings which are necessary to adapt to changing air conditions and to avoid possible threats.
  • A complex series of motor responses must be initiated which help direct the fly to its target – something like the game of “hot and cold” – if the scent becomes weaker when veering left, the fly must then veer right.
  • Once the target has been reached, the fly must then initiate the process of feeding which entails the operation and coordination of salivary gland outputs, movement of mouthparts, and gustatory reflexes which suck up the food.

Each of these behaviors must be supported by the precise wiring of neurons in the fly’s brain which provide the necessary motor responses in accord with sensory inputs to result in survival. This in turn must be supported by genetic coding which is responsible for getting all these neurons in their proper place and have all the appropriate connections. It is not singular genes which are responsible for this structure, but entire gene regulatory networks (GRN).

613 neurons from one portion of the fruit fly’s brain, with artificial colors assigned to each neuron to make them easier to follow in the dense tangle of connections. Image credit: The FlyEM team,

The first challenge to an evolutionary explanation is the fact that many of these innate behaviors would need to be in place at the same time for the fly to survive. For instance, the signaling about the concentration of acetic acid would confer no advantage to the fly unless there first was a processing unit which could direct an appropriate response. The response mechanism such as directed insect flight would not confer an advantage unless it could first receive a message about acetic acid.

The processes of evolution ostensibly operate by the gradual changes of singular existing genes which are tested for success by natural selection. If a mutation cannot promote survival without the existence of some other mutation, then it will not persist in the genome. Getting one positive mutation is difficult enough, but getting two positive coordinated mutations is a stretch.

Each of these innate behaviors is tied to a separate set of neurons and synapses in the brain which are formed due to separate sets of GRNs which are tied to a multitude of individual genes. When one considers the enormous number of possible arrangement of neurons and all the possible connections which must be made between them to generate these innate behaviors, the search space for success by random mutations of genes becomes intractable. A more likely explanation for such arrangements would be the act of intelligent agency – not simply because of the improbabilities involved, but because such arrangements closely parallel the intelligent agency of humans.

In the computer sciences, people develop input and output devices which interact with a central processing unit. Input devices (like the fly’s antennae) convert some stimulus into a variety of electrically generated binary coded messages. The CPU (like the fly’s brain) sort out these binary codes, and generate a different binary code. This process requires both hardware and software to function – wiring (neurons) upon which to transmit the messages, and programming (arrangements of synapses) which produce and transmit binary code based on the input. The output device (like the fly’s flight mechanisms) must be able to convert the binary coded message from the CPU into some action.

From our human experience, we know hardware and software are not derived from a box of jumbled wires thrown in a box like the Christmas lights. Instead, it requires distinct foresight, planning and designing to set everything in the right place. The proper functioning of an input device does not dictate the proper functioning of an output device, but if either fails, the other fails as well. The signaling about acetic acid does not implicitly control muscle contraction, and when muscles do contract, they do not “know” where they are going. Success here depends on foresight which is sorely lacking in the purposeless nature of random mutations.

What we find in even the relatively simple brain of a fly is a set of complex interdependent systems which functionally require both hardware (sensory and motor neurons) and software (properly arranged synapses) to operate. Such systems are best explained by the work of intelligent agency – that there is a mind behind the existence and functioning of the brain of a fly. Random mutations on an organism’s nucleic acids could not reasonably produce this level of complexity and multi-system integration.

[1] Emily Anthes, “Why Scientists Have Spent Years Mapping This Creature’s Brain” Accessed 11/23/21.

[2] For example, see: Li G, Hidalgo A. Adult Neurogenesis in the Drosophila Brain: The Evidence and the Void. International Journal of Molecular Sciences. 2020; 21(18):6653. as well as Contreras, E.G., Palominos, T., Glavic, Á. et al. The transcription factor SoxD controls neuronal guidance in the Drosophila visual system. Sci Rep 8, 13332 (2018). Both accessed 11/23/21.

[3] In the study regarding the gene regulation in development of visual systems, the researchers note that the SoxD in fruit flies has similar function to the Sox5 gene in mice in neuron migration, and thus infer that SoxD is “evolutionary conserved”. However, when one considers the vast difference in visual systems and optic lobe structure between arthropods and vertebrates, and that the common ancestry between these two groups is virtually untraceable, it seems as equally tenable (if not more so) that a common designer is a better explanation than a common ancestor for this similarity.

[4] Jouandet, Genevieve C, and Marco Gallio. “Catching more flies with vinegar.” eLife vol. 4 e10535. 9 Sep. 2015, doi:10.7554/eLife.10535. Accessed 6/7/22. Note: if the signal is too strong, it will indicate too many of the sugars have been converted into acetic acid, and will not be an appropriate food source for its offspring.

3 thoughts on “The Mind Behind the Brain of a Fruit Fly

  1. cchristianssen June 11, 2022 — 1:57 pm


    Were there suppose to be hyperlinks “here”:

    The fly must be able to initiate flight which itself defies an evolutionary explanation (see here, here and here). More than just becoming airborne, the fly must be able to control its direction of flight. Also. This research begs the question about the human intellect required to create a device that could capture an image of a portion of something the size of a poppy seed. And then even understand what you are looking at. And then be able to communicate that to other humans. Could any other creature on this planet besides a human create such a thing or do these other things? And how is the human brain capable of inventing such a thing and processing that information? Evolution — Not!!


    Curt Christianssen (Mr C) Sent from my iPhone



    1. For the sake of comparison, the mouse brain has about 70 million neurons while the human brain has around 86 billion!


    2. Thanks. Hyperlinks added. Please do me a favor and “like” the link on Facebook


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