Examples of Recurring Design Logic in Living Systems

[00:00:00] Speaker A: Hey, everyone. A quick heads up before we get to today's episode. This fall, Discovery Institute Academy will be offering both high school biology and high school chemistry for the coming school year. These high quality online courses are designed especially for homeschool students. They cover the fundamentals of biology and chemistry and also introduce students to the powerful evidence of intelligent design in nature. The courses include video lectures, readings, lab activities, assignments, and more. They're designed to make it easy to teach science to your kids. There are options with a live science teacher and an option that is completely self paced. Even if you don't have kids who can participate. Can you help us get the word out to those who do? For a limited time, parents who register their student can get $50 off tuition. These courses are a wonderful way to raise up the next generation of scientists. Scientists who understand that we and our universe are intelligently designed. For more information, visit DiscoveryInstitute Academy. That's DiscoveryInstitute Academy. [00:01:08] Speaker B: Idaho. The Future, a podcast about evolution and intelligent design. [00:01:15] Speaker A: Well, have you ever stopped to think about the incredible complexity that's packed into even the tiniest forms of life? What if I told you that a single celled bacterium manages its internal affairs with a level of precision and coordination that rivals a sophisticated factory? Like turning genes on and off in perfectly timed sequences. It's a universe of intriguing and intricate machinery, all happening invisibly right around us. Well, today we're diving into the astonishing microscopic world with my guest, Dr. Jonathan McClatchy. Dr. McClatchy is a resident biologist and fellow at Discovery Institute's center for Science and Culture. And he's been writing extensively about what he calls recurring design logic in these complex biological systems. He argues that the way these bacterial systems are organized with genes activating in a specific ordered manner, looks remarkably like the product of intelligent engineering. Based on his recent articles, we'll explore fascinating examples of, like how bacteria build their tiny motors, survive extreme conditions, and even talk to each other to coordinate the expression of toxins. So, time to buckle up for a mind bending journey into the unseen ingenuity of the bacterial realm. Hey, Jonathan, thanks for joining us. [00:02:33] Speaker B: Great to be here. [00:02:35] Speaker A: Well, you've written recently at evolutionnews.org, our flagship news and commentary site on examples of recurring design logic in biological systems. Now, first, let's start with the basics. Tell us what you mean by recurring design logic and give us a few examples of it in everyday life. [00:02:54] Speaker B: Yeah. So throughout diverse biological systems, we often see these recurring themes or logic that pop up over and over again. And this is the sort of thing that we might expect to see in engineered systems. When we look at a building, for example, we recognize different architectural features that are associated with a particular architect. Or when we look at a painting, we see particular features that are the hallmark of that particular painter, that particular painter's work that characterize it. There are even aspects of an author's writings that are distinctive of that individual writer. So these are the sorts of phenomena that we expect to see in a designed system, rather than systems that arose incrementally by chance and physical necessity. [00:03:53] Speaker A: Yeah. Okay, so another word might be patterns of thinking that you would see in different intelligent agents. Okay, that makes sense. Now, is the discovery of recurring design logic even across systems that don't appear related. Is that surprising or something we'd expect. [00:04:11] Speaker B: To see on the hypothesis of design? It seems to me that that is something which is really a prediction of the hypothesis, because as I said, we find routinely that when we inspect engineered or designed systems, we see these recurring design themes or recurring logic that crops up over and over again. Whereas on the falsity of the design hypothesis, on a hypothesis of evolution that is unguided and mindless and devoid of teleology, it seems to me that that is something that's quite surprising, that you'd have these different diverse systems which are not evolutionarily descended from one another, that would exhibit the same sorts of recurring design logic that's implemented in different ways. [00:05:08] Speaker A: Yeah. Okay. Well, let's jump into some examples and you lay some out in your coverage of this particular topic. The first is something called two component regulatory systems. Now, what are these systems? What are the two components, and what general purpose do they serve for bacteria? [00:05:25] Speaker B: Yeah. So bacterial cells use two component systems to sense and respond to changes in the environment. And we find those throughout bacterial organisms. That is very, very common in the prokaryotic world. And as their name implies, two component systems essentially have two major components. You have the sensor histidine kinase and a response regulator. And the sensor kinase, in response to chemical cues, undergoes autophosphorylation, which means that a phosphate group is transferred from ATP to a histidine residue on the kinase. And the hesidine kinase has itself two domains as an input domain and a transmitter domain. And the input domain is located on the cell's exterior, so outside of the cell, and it's particularly situated to detect incoming environmental signals. And the transmitter domain is situated on the cytoplasmic face of the cell membrane. And so it's positioned so that it can interact with the response regulator. So the phosphate group that. Remember I mentioned that the hesidine residue of the response of the hesiodine kinase gets phosphate group transferred to it from ATP and then this phosphate group in turn is transferred to the response regulators. That's the second component of the two component system, which then drives a cellular output such as turning genes on and off, etc. And so, as I mentioned before, two component regulatory systems are extremely common among bacteria and each utilizes the same basic design logic, even though these are not evolutionarily descended from one another. [00:07:22] Speaker A: Okay, all right, that's a good basic breakdown of it. So you've got a sense and response system that is common across different organisms, even wildly different organisms, as you've pointed out. Now, you give the example of E. Coli regulating outer membrane proteins in response to environmental osmolarity using a two component system like you're describing, how does this system allow the bacterium to sense changes in its surroundings and then respond appropriately? [00:07:54] Speaker B: Yeah. So osmolarity is essentially a measure of the concentration of solute particles in a solution. And the cell needs to regulate the expression of porins in response to this environmental osmoregularity. And it does so by means of a two component system. So in this case, the sensor kinase is, is a protein called MZ and it's located in the inner membrane. And MZ detects osmolarity changes and it undergoes autophorylation. And then the response regulator for the system is known as ompr, and it receives the phosphate group from MZ and it regulates the expression of genes. So when osmolarity is high, the kinase activity of MZ is activated and this results in the phosphorylation of ompr. And when osmolarity is low, the phosphatase activity of MZ is activated and this reduces the levels of phosphorylated ompr. So when OMPR is phosphorylated, it becomes an active dimer that has enhanced DNA binding ability. That's specific to OMPC and OMPF gene promoters. These are porin genes that incur code outer membrane proteins which allow the passage of metabolites across the outer membrane of gram negative bacteria. Gram negative bacteria are bacterial cells that have two membranes, an inner and outer membrane. So the pore diameter of OMP F is larger than the pore diameter of OMP C. So this allows for a tenfold faster diffusion rate, which is advantageous under conditions of low osmolarity where there are scarce nutrients. If osmotic pressure is low, the Synthesis of omp F is increased, whereas if the osmotic pressure is high, the expression of OMPC is increased and also the transcription of MyCF antisense RNA is initiated. And this essentially blocks the transition of OMPF by complementary binding and that represses the synthesis of ELMP F. So this is controlled by a two component system making use of a sensor kinase as well as a response regulator. [00:10:21] Speaker A: Okay, yeah. And that's a good dose of technicality, as it were. And I always hope that, you know, the people that are listening or watching are not going to get scared away by the technical details. As Michael B. He challenges us in Darwin's black box. You know, we've got to bite the bullet of complexity if we want to understand why Darwinian evolution is not capable of this. So, audience, stay with us. This, you know, we really do need to get into the technical aspects of this a little bit just to understand why. So Jonathan can always depend on you for that and I'm grateful for that. Okay, so another example that you've laid out is something called chemotaxis, and that's quite a fascinating example in itself, especially the idea that bacteria have kind of a memory system for chemical concentrations. Can you explain how that system works and how it helps bacteria navigate their environment? [00:11:21] Speaker B: Sure. So chemotaxis is really a signal transduction system that enables bacterial cell to move towards attractants like glucose or away from poisons. And it does so by modulating the frequency of runs and tumbles. So basically the flagella of the bacterial cell rotate as a bundle and their default is to rotate in a counterclockwise way. But in response to chemical stimulus, it can switch direction and start spinning clockwise. And this results in the bacterial flagellar bundle breaking apart and that results in the bacterial cell tumbling. And if you are moving towards a food source like glucose, then you want long runs and less frequent tumbles so that you can move in the direction of that food source. Whereas if you're moving towards a poison or you're moving away from a food source, then you want to have frequent tumbles and shorter runs so that you can reorient yourself and sample the environment and trying to get closer to that food source or away from the poison. And the chemotaxis system is again a two component system. So in this case, so you have embedded in the cell membrane, methyl accepting chemotaxis proteins and different methyl, excepting chemotaxis proteins, which are also known as mcps, can detect different types of molecules and they're able to bind attractants or repellents. And these receptors then communicate with and activate the so called key proteins. And so there are proteins called key A and key W which are bound to the receptor. Key W essentially functions as an adapter protein. But key A is what we call the sensor kinase or histidine kinase for this system. And so, upon activation of the receptor, the conserved histidine residue of key A undergoes artifice florylation by adp. So it obtains a phosphate group and there are actually two response regulators called key B and qylon. And there's a transfer of a phosphoryl group to the conservative residue from key A. So key B and Q both receive a phosphate group from key A and then the QY protein subsequently interacts with the flagellar switch protein that's known as fly M and that induces the switching inflagellar direction from counterclockwise to clockwise. And so this is again a two component system which is analogous to the system that we reviewed previously regarding osmoregulation. [00:14:31] Speaker A: Yeah, yeah, it's quite fascinating. And so the memory system then, at least in bacteria here in this example, basically it's a system of chemical responses and stimuluses or stimuli based on the environment. Is that what constitutes the memory system here? [00:14:53] Speaker B: That's right. And as I said, there's a second response regulator. So we've looked at key Y, there's also one called key B, which as I said also obtains a phosphate from key A. And that in turn that response regulator acts as a methyl esterase. So it functions to remove methyl groups from the receptor or from the methyl accepting chemotaxis protein, the mcp. And it works antagonistically with another protein called hr, which is a methyltransferase, which adds methyl residues to to the, to the mcp. So if the level of attractin is high, the level of phosphorylation of key A and therefore by implication or by extension key Y and key B remains low and the cell swims smoothly and the level of methylation of the mcps will increase because there's no key B, there's no activated key B to demethylate the mcp, and the mcps no longer respond to the attractant when they're fully methylated. So even though the level of attractant might remain high, the level of key A, level of phosphorylated key A, that is, and level of phosphorylated key B increases and the cell begins to Tumble and the MCPs can be demethylated by the phosphorylated key B. And. And when that happens, the receptors can once again respond to attractants. So this regulation allows the bacterial cell to remember chemical concentrations from the recent past a few seconds and then compare them to those that is currently experiencing and thus know whether it's traveling up or down a gradient. [00:16:54] Speaker A: Okay. Yeah, I think I've got it now. Well, there's something else. I mean, we think that's cool, you know, memory system and bacteria. What about actually talking to each other? There's something called quorum sensing in bacteria. How does that allow these populations to coordinate their actions? And what are some real world implications of this ability? [00:17:15] Speaker B: Yeah, so quorum sensing is a mechanism by which a bacterial cell is able to sample or the bacterial population is able to sample population density. And there's a number of purposes for this. For example, if you're a lone bacterial cell, it doesn't make a lot of sense for you to start secreting poisons because it's not really going to do you a lot of good. In fact, it's going to trigger the cell's immune response. So you only want to start secreting poisons when there's. When your population density exceeds a certain threshold, or if you're a bioluminescent bacterial cell, it doesn't make a lot of sense for you to glow when there's only one of you. It makes more sense when there's a whole population that's exceeding a certain threshold. So each species employs quorum sensing, which includes most gram negative bacteria. So gram negative bacteria, bacterial cells that have two membranes, and also some gram positive bacteria, which only have a single membrane, synthesizes a tiny signal molecule that's known as an autoinducer, which diffuses freely across the cell's membrane. Autoinducers are specific to particular species, which means that each cell of the same species makes the same molecule. This means that the autoinducer is only present in high concentrations inside the cell when there are many cells of the same species nearby. Because then if there's a certain. If the population density exceeds a certain threshold then increases greatly that the autoinducers are going to re enter the cell. And inside the cell, the autoinducer binds to an activated protein, and the activated protein is specific for that particular molecule and thus signals that. So it signals that the protein to begin transcription of particular genes. So, for example, in the case of one of the most famous. In fact, the first discovered example of quorum sensing was discovered by Bonnie Bassler, who's A microbiologist is Quorum sensing in vibrator Fischeri is kind of the model system for studying quorum sensing. And the light that this species of bacteria emits results from the action of the enzyme luciferase. So an activator protein that's called LUX R is responsible for controlling the LUX operons. So an operon is a collection of genes that are under control of a common promoter which are in turn responsible for the transcription of the proteins required for luminescence. And these operons are induced when the concentration of the autoinducer specific to Vibrio fischeri reaches a high enough concentration. And this autoinducer is self synthesized by the enzyme, which is encoded by the LOX I gene. So quorum sensing is very widespread, particularly in gram negative bacteria. So Zidomona zebruginosa, for example, uses such population sampling processes to trigger the expression of a significant number of unrelated genes when the population density reaches a certain threshold. And these genes allow the cell to form a biofilm, which increases the pathogenicity of the organism and also prevents the penetration of antibiotics. So it has wide application. But again, the system is mediated by a two component system. [00:20:41] Speaker A: Okay, yeah, I was going to ask, is this another example of that two component system that you see? And indeed it is. Well, let's talk about another example of recurring design logic that you've laid out. And that's something called transcriptional hierarchies. Why is it a crucial concept in understanding how bacteria work? [00:21:01] Speaker B: Yeah. So transcriptional hierarchy is a regulatory system in which genes are expressed in a specific order sequence, ensuring that the appropriate genes are activated at the right time and in the proper order. So an example of a transcriptional hierarchy would be flagellar assembly. And there's different ways that that works out. But in Salmonella, which is a model system for studying flagellar assembly, you have a defined mechanism that determines that you're not going to start producing the propeller, the filament of the flagellum before you finish constructing the hook basal body apparatus. And so, and this is governed by a transcriptional hierarchy that ensures that only the appropriate genes are expressed at the appropriate time. [00:21:44] Speaker A: Now, the bacterial flagellum in Salmonella, that's, that's an incredibly complex process. And as you say it, a lot require a lot depends on how it's put together and in what order. So can you break that down in simple terms, just that assembly process and how it's regulated by these hierarchies? [00:22:03] Speaker B: Sure. So there are in Salmonella, which As I said, is the model system for studying flagellar assembly. There are three classes of genes. You have class one genes, class two genes, and class three genes. So class one genes, you've got basically two genes called flu D and flu C. And their products come together to form what's known as the enteric master regulator. And then that goes and drives the expression of of the class 2 genes, which are comprised of 35 different genes over 8 operons. Remember, an operon is a collection of genes that are under control of a common promoter and that these protein products essentially are responsible for putting together the hoop basal body apparatus. And among the class two genes are two genes in particular, known as flea, which codes for a sigma factor called sigma28, which regulates RNA polymerase, and another gene called flag M, which codes for an anti sigma factor. So anti sigma factors, as their name suggests, inhibit the function of sigma factors. And so, as the needle complex is being completed, there is an interaction that takes place inside the needle or the type 3 secretion system, which triggers for the flag M to be exported out the type 3 secretion system. And this then liberates Sigma 28 to go and drive the expression of the class 3 genes by binding to the RNA polymerase. And so the class 3 genes code for the propeller, otherwise known as the filament, the motor force generators, chemotaxis proteins. And so that ensures the timely expression of the different sets of proteins involved in flagellar assembly. So you don't have the propeller being assembled before you've completed the hook basal body apparatus. So it's a very elegant mechanism, and this is a prime example of what we might call a transcriptional hierarchy. [00:24:13] Speaker A: Okay, well, moving to another example that you lay out, you discussed sporulation in bacillus subtilis. So tell us about that and why that's important to this discussion. [00:24:26] Speaker B: Yeah, so sporulation, or endophore formation, is a process whereby a vegetative cell differentiates into an endospore, which is a highly resistant, dormant structure that can withstand extreme stress, such as heat, desiccation, UV radiation. And that process is triggered by nutrient starvation. So once sporulation has been initiated, the chromosomes align along the longitudinal axis of the cell, known as the axial filament. And the cell then divides asymmetrically near one of the poles, and that forms the smaller force bore and the larger mother cell. And the membrane of the mother cells engulfs the force bore, such as it completely envelops it, and then a thick layer of heptaglycan Known as the cortex, is deposited between the four spore membranes. And this is critical for dehydration and dormancy. And physical and chemical resistance is conferred by proteinaceous layers known as spore coats, which assemble around the cortex. And then eventually the mother cell undergoes apoptosis or cell death, which releases the mature spore. And just like flagellar assembly, sporulation is under the control of a transcriptional hierarchy where you have sigma factors to promote the expression of specific sets of genes and so forth. [00:25:55] Speaker A: Okay, so another example of that hierarchy, which is very important in life, and we're seeing it across lots of different systems now, across all of these systems that you're mentioning, you emphasize recurring design logic. So why do you see this as surprising from an evolutionary perspective? And what does it suggest to you about the origins of these biological systems? [00:26:18] Speaker B: Right, so these systems evolved by chance and physical necessity, and bear in mind that these are not descended from one another. Then it seems quite surprising that you'd get these recurring design themes and ideas recurrent over and over again. But this is exactly what we find in not just one or two instances, but throughout biology. We see these recurring design themes, recurring design patterns, recurring design logic. And this is precisely the sort of thing that we expect to see in engineered or designed systems, but not particularly at all what we'd expect to see for evolved systems. And so it tends to support an engineering perspective on biology rather than an evolutionary one. [00:27:03] Speaker A: Right. Well, Jonathan, thanks for stopping by today to give us a little bit of that technical detail underneath this amazing class of evidence that you're identifying this recurring design logic in living systems. Definitely another class of evidence for intelligent design in nature. So thanks for, for catching up with me. [00:27:23] Speaker B: Absolutely great to be here. [00:27:25] Speaker A: Well, audience, if you enjoyed this deep dive into the complexity and design at the heart of life, there's actually plenty more where that came from. Jonathan and I have recorded a slew of conversations unpacking numerous biological systems that exhibit evidence of intelligent design. We've done episodes on muscles, hearing our digits, the origin of our fingers and toes, obviously the blood clotting cascade. We did a three part series on sexual reproduction and why that's such a spicy problem for Darwinian evolution. We've looked at the life friendly properties of water and sunlight, and that's not even counting our chats about Bayesian reasoning and how we can apply that to a cumulative case argument for intelligent design. So lots to go back and check out. If you haven't listened to those or watch them, you'll find all those episodes and many more at our website, id the future.com or through your favorite podcast platform. And don't forget, id the future now has its own channel on YouTube. So look that up and subscribe. Help us spread the word about it. You can find it at YouTube.com d the future YouTube.com d the future. Well, for the podcast, I'm Andrew McDermott. This is Dr. Jonathan McClatchy. We'll see you next time. [00:28:42] Speaker B: Id the future, a podcast about evolution and intelligent design.