Researchers claim to have found a math basis for predicting evolution

_{Denyse O'Leary

February 18, 2021

Evolution, Intelligent Design, Mathematics}

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Scientists created a framework to test the predictions of biological optimality theories, including evolution.
Evolution adapts and optimizes organisms to their ecological niche. This could be used to predict how an organism evolves, but how can such predictions be rigorously tested? The Biophysics and Computational Neuroscience group led by professor Gašper Tkačik at the Institute of Science and Technology (IST) Austria has now created a mathematical framework to do exactly that.
Evolutionary adaptation often finds clever solutions to challenges posed by different environments, from how to survive in the dark depths of the oceans to creating intricate organs such as an eye or an ear. But can we mathematically predict these outcomes?
This is the key question that motivates the Tkačik research group. Working at the intersection of biology, physics, and mathematics, they apply theoretical concepts to complex biological systems, or as Tkačik puts it: “We simply want to show that it is sometimes possible to predict change in biological systems, even when dealing with such a complex beast as evolution.”
Institute of Science and Technology Austria, “Can evolution be predicted?” at ScienceDaily

The paper is closed access.

We’ll wait till they make a number of predictions and then see if they come true.

Comments

Why evolution in principle cannot create functional things in biology? It's simple. If we take a look at whatever biological system, we will immediately notice that the components of this system must fit interrelated components. That is, they must have the right shape and size, otherwise the function of the system cannot be performed. In genetic sense it could be said that genes that encode these components must be specific. For e.g. if we replace the genes that encode the heart valves with junk genes or genes that encode human ear, the cardiovascular function would be lost. And the only way to get the function back is by changing the genes towards specificity that fits interrelated components of the heart, such as the atrium. Achieving this specificity, however, is an insurmountable obstacle for the evolution process. This is due to two physical constraints: the lack of changes; and the lack of causality for functional assembly. Let's now practically demonstrate these two constraints. For that purpose, we will use the mechanical gear system. This system was discovered back in 2013. in the small hopping insect Issus coleoptratus. The insect uses toothed gears on its joints to precisely synchronize the kicks of its hind legs as it jumps forward. Suppose that evolutionary development of this system is underway and all of its components (trochantera, femur, coxa, muscles, ...) are in existence, except the toothed structures. As with any system, its components must be shaped so that they fit interrelated components. So in order for this system to provide the synchronization and rotation function, evolution must reshape some pre-existing structures into toothed structures. Once these structures appear they will provide an evolutionary advantage and be naturally selected. Now, how is evolution going to do the reshaping job? Well, there is only one way. By changing the DNA. This is the only possible way for evolution to reshape anything, given that biological structures are encoded in genes. In reality, the toothed structures are the culmination of the interaction of many different genes over many generations of cell division. But here we will be extremely conservative and assume that these structures are encoded with only one average eukaryotic gene. So, what evolution actually has to do in the reshaping job is finding a gene with specific nucleotide sequences. The number of such sequences if extremely large given that there can be many micro-deformations of toothed structures and their distinct shapes that will all fit each other and interrelated components, and in that way, provide the said function. Lets's call these sequences - the target sequences. However, the number of unfitting structures is even larger. Just try to imagine all the possible shapes and sizes of non-gear structures. Now imagine all the micro-deformations of these structures. Now imagine all the micro swaps that produce equal macro structures. Thus, the number of unfitting structures is unimaginably large. Lets's call the sequences that encode these unfitting structures - the non-target sequences. Now that we have defined the target and non-target sequences, we can start calculating whether evolution can produce enough changes in order to find the target ones. The first parameter required for this calculation is the replacement tolerance. The replacement tolerance is the degree by which a gene can tolerate random nucleotide replacements before losing its function. In our case, this function is the ability of the toothed structures to fit both each other and other interrelated components. Some gens can tolerate many such replacements. On the other hand, the so called ultra and highly conserved genes, must be very precise to retain their functions, and even a few replacements are detrimental. In our calculation we will use extremely high replacement tolerance of 60 percent. That means that when our gene is in a functional state, 60 percent of its nucleotides can undergo random replacements without causing the loss of function. Obviously, accurate transmission function requires gears to be precise. So, our replacement tolerance of 60 percent in not realistic. But, we want our calculation to be beyond any doubt. The second parameter is the length of the gene. For an average eukaryotic gene this is 1,346 base pairs (bp) of nucleotides. Now that we have the parameters we can apply simple mathematical operations and perform the calculation. Given that there are four types of nucleotides (adenine (A), thymine (T), guanine (G), and cytosine (C)), the number of all possible sequences of length 1,346 is 4^1,346 = 10^810. With the 60 percent replacement tolerance, we get that the number of target sequences is 4^(1,346*0.6) = 10^486. To get the non-target sequences we simply subtract the target ones from all possible sequences (10^810-10^486). By dividing the result with the number of target sequences, we get that only one out of 10^324 sequences is target sequence ((10^810-10^486)/10^486). In other words, evolution would have to produce 10^324 changes just to find one target sequence. But is evolution capable of doing that? Unfortunately not. This task is physically impossible for evolution even with our extremely conservative assumptions. This is because the theoretical maximum of changes that the universe can produce from its birth to its heat death, is approximately 10^220 (the number of seconds from the big bang until the heat death multiplied by the computational capacity of the universe). Even with the absurd assumption that toothed structures can tolerate 80 percent deformation, evolution would have to produce 10^163 changes. And this exceeds the computational capacity of the whole universe from its birth to the present day. So, the lack of changes represents the first physical constraint that makes it impossible for evolution to achieve the above said specificity. But let's now ignore the above constraint. Let's assume that target sequences are found and that DNA contains all the genes necessary for the gear system to work. Does that mean we have a working system? Unfortunately not. Having the right genes stored in the DNA is like having the right engine components stored in a warehouse. Just because they exist, that doesn't mean they will spontaneously assemble themselves into a functional engine. No causality for such an assembly exists in nature. Evolution is not aware that functionally interrelated components exist and must be assembled together to provide better survival to the organism. Nor evolution has or would be able to use the assembly instructions. So, just having the right genes stored in the DNA, won’t make them to spontaneously express themselves at the right place and in the right time. Nor would that make their products to assemble themselves the right way into the functional whole. Evolution is capable of changing the genes, the same as corrosion, erosion or other natural processes are capable of changing the components of non-living systems. However, these processes are incapable of bringing separate components together into a logical and coherent system that will perform useful work. Therefore, the lack of changes and the lack of causality for functional assembly, are the reasons why evolution cannot create functional things in biology.forexhr_{February 19, 2021
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Evolution is both, a fact and a flat-earth-like theory. First, why it is a fact? Well, because evolution is defined as hereditary changes (mutations) whose frequencies fluctuate based on environmental factors (natural selection). Obviously, mutations and natural selection do happen. So evolution as a process is indeed a fact. Second, why it is a flat-earth-like theory? Because evolution as a theory imagines that evolution process rapidly produced major biological transitions that are seen in the fossil record. These transitions include the origin of novel organs, organ systems or body planes (for e.g. Cambrian explosion), or going from land to water in 15 million years (dog-like mammals into whales). In reality however, that what is imagined in the theory is contradicted by all possible instances of observation. Namely, all the existing species are continuously under evolution process. That is, they are undergoing hereditary changes whose frequencies fluctuate based on environmental factors. In many of the species this process operates way longer than the Cambrian explosion event or the event of turning dog-like mammals into whales. Yet, no population within the existing species neither underwent nor is undergoing major biological transition. Take humans for example. Human species arose approximately 6 million years ago. Since then, we have undergone a lot of evolution. We have undergone a lot of hereditary changes and fluctuations of their frequencies. Yet today, no human population exists that is undergoing, let alone underwent, major biological transition. Meaning, no population has been observed that would have some novel organ, organ system or body plan, like Cambrian species had. Nor evolution caused some populations to become aquatic, that is, to be able to survive and reproduce entirely in water. Moreover, no human population shows even traces that such transformations have started to happen. Even when change, such as webbed fingers happened in an individual - which the theory imagines is the first step towards the flipper-like organ, this never got spectated into a separate human subspecies and became the norm, that is, a fixed trait. Rather, it always ended up being just an abnormality that lead to an evolutionary dead-end. The same is true for all other species, regardless of how long have they been around. Lemurs have been around for some 40 million years. Fig wasps, rats, crocodiles, coelacanths and nautiluses 60, 100, 200, 350 and 500 million years respectively. But again, all the individual changes lead to evolutionary dead-ends instead of becoming traits. That is why not a single population within these species underwent nor is undergoing major bio-transition. So regardless of time, evolution process literally never produces major biological transitions. That means, first, that evolution is not the cause of the transitions seen in the fossil record. Second, that the theory of evolution imagines the opposite to what is observed in reality. Imagining the opposite to what is observed in reality is being a flat-earth-like theory. Given what we have said, it logically follows that major biological transitions were designed. Given the fossil record, it logically follows that in the creation of species the designer decided to use the DNA of pre-existing species to create novel species. Because, this is how design operates. New things are not created from scratch but are rather just updated with new functional information. That is why we observe, for e.g., shared ERVs among different species. Or the progression from a land animal to whales in the fossil record. In the creation of whales the designer simply decided to use the DNA of some pre-existing land animal to see what kind of aquatic animal would turn out. So both, the fossil record and patterns observed in the DNA, are in line with the theory of intelligent design, and in the same time they falsify the theory of evolution.forexhr_{February 19, 2021
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We didn't get whales by small, gradual changes to some pre-existing animal. We got POOF!, "Here's a whale for ya, lad!" Or, more interestingly, there are both Pacific and Indian Ocean poisonous Sea Snakes. Externally, they look VERY similar. Internally, the are NOT genetically related. How can that happen randomly? So my suggestion remains that we spend more time studying "Hitchhiker's Guide to the Galaxy-- 'Norway was a country on Earth that was a particular love of its creator, the Magrathean Slartibartfast, who rhapsodises over its "lovely crinkly edges". For a time in the distant past, fjords were fashionable and he won an award for their design. Sadly, however, trends, even in planetary design, changed, and they fell out of favour.' So there you have it. Certain types of "stuff" (a technical term) get pumped out by the design staff for a bit. But then tastes change, and all the new planets get coral reefs.mahuna_{February 19, 2021
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They only get away with this kind of B.S. because "evolution" is used equivocally and most people don't realize that. Blind Watchmaker "evolution" writ large remains bunk.Concealed Citizen_{February 19, 2021
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The hype in the article implies that Mathematics will now be able to predict Darwinian evolution creating eyes and ears,,,
Evolutionary adaptation often finds clever solutions to challenges posed by different environments, from how to survive in the dark depths of the oceans to creating intricate organs such as an eye or an ear. But can we mathematically predict these outcomes?
Hey, mathematically predicting the creation of eyes and ears by completely unguided Darwinian processes would be worthy of several Nobel prizes. Get the Champagne ready! Yet the reality of the situation follows in the very next paragraph, "We simply want to show that it is sometimes possible to predict change in biological systems, even when dealing with such a complex beast as evolution."
This is the key question that motivates the Tka?ik research group. Working at the intersection of biology, physics, and mathematics, they apply theoretical concepts to complex biological systems, or as Tka?ik puts it: "We simply want to show that it is sometimes possible to predict change in biological systems, even when dealing with such a complex beast as evolution."
Hmm, let's just say that this movie is, in very short order, NOT living up to its hype. Reality sets in even further later in the article,
They developed a statistical framework that uses experimental data from complex biological systems to rigorously test and quantify how well such a system is adapted to its environment. An example of such an adaptation is the design of the eye's retina that optimally collects light to form a sharp image, or the wiring diagram of a worm's nervous system that ensures all the muscles and sensors are connected efficiently, using the least amount of neural wiring.
So the article, in a few short paragraphs, went from the over the top hype of being able to mathematically predict, via Darwinian evolution, the creation of eyes and ears, to merely being able to quantify how well such a system may be adapted to its environment. Nice work sure, but color me very much unimpressed as to the over the top hype that accompanied the mathematical work. Moreover, this mathematical work is not really all that original but stems from previous mathematical work that was first done by William Bialek at Princeton University.
Gašper Tka?ik himself was inspired to study complex biological systems through the lens of physics by his PhD advisor William Bialek at Princeton University.
William Bialek's previous work is, to put it mildly, certainly NOT friendly to Darwinian presuppositions. To quote the following article, "Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark,,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants."
William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them;,, the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head;,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html
To make the dilemma for Darwinists even clearer, the following article states that, ""I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.,,,"
Math sheds light on how living cells 'think' - May 2, 2018 Excerpt: "Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to 'think' --,,, "We could never hope to measure the full complexity of cellular networks -- the networks are simply too large and interconnected and their component proteins are too variable. "But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.,,, Dr Araujo's work has focused on the widely observed function called perfect adaptation -- the ability of a network to reset itself after it has been exposed to a new stimulus. "An example of perfect adaptation is our sense of smell," she said. "When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present. "Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very feint and very strong odours. "This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals -- hormones, growth factors, and other chemicals -- and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there. "I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.,,, Professor Lance Liotta, said the "amazing and surprising" outcome of Dr Araujo's study is applicable to any living organism or biochemical network of any size.,,, https://www.sciencedaily.com/releases/2018/05/180502094636.htm
So the burning question now becomes, since there are "a surprisingly limited number of ways a network could be constructed to perform perfect adaptations', then how in blue blazes did unguided Darwinian processes, time after time, happen to stumble upon the just right 'perfect' solution' to construct a system that "couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants"? Moreover, it does not take a mathematical genius to predict what will happen if you make changes to a system that is ALREADY perfectly adapted to its environment. It will degrade in its functionality. PERIOD! Calling Dr. Michael Behe, i.e. "Darwin Devolves"!bornagain77_{February 19, 2021
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If it's "sometimes possible" to predict a change, the prediction is not a theory or a formula or a model. The prediction is just a coin-toss. I can "sometimes predict" tomorrow's weather by using a random-number generator with segments of the number line labeled as rain and snow and sun and tornados. This is not a model or a theory, it's just a waste of time. I'd rather look at the radar or trust my internal senses.polistra_{February 18, 2021
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Adaptation is not the same as evolution. Evidence does exist for adaptation, but not evolution. Speciation has never been witnessed anywhere in nature, no matter how controlled the test might be to try to force evolution, it remains adaptation every time.BobRyan_{February 18, 2021
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