Homology explains phylogeny(except when it doesn't)

Theory of Convergent Evolution Analyzed

Evolution News & Views May 11, 2015 3:04 AM 

The knifefish, rather than having several fins like a trout, has one long "ribbon fin" that undulates along the length of its body. Studies of its motion reveal that it uses the optimal wavelength to get the most forward thrust, stability, and maneuverability out of its investment of energy. But the knifefish is not alone: the same optimal design can be found in cuttlefish (cephalopods), rays (cartilaginous fish), certain flatworms, and other bony fish that are evolutionarily unrelated. In fact -- if evolution by natural selection is assumed to be the cause -- this design emerged independently at least eight times. To the Darwinian, it's another remarkable case of "convergent evolution."

A paper in PLOS Biology investigates this phenomenon and tries to explain it. The five authors, primarily from Northwestern University, used a robotic knifefish to nail down the physical factors related to optimal swimming design: the length of the fin's undulation and the mean amplitude. Dividing the one by the other yields what they call the Optimal Specific Wavelength (OSW). Then they measured the OSW on 22 live swimmers, such as cuttlefish and rays, to see how they rated. They found that the values "converge to a narrow range" around 20, even though the animals belong to eight separate groups whose presumed ancestors did not possess this kind of propulsion. Robin Meadows says in a companion piece likewise in PLOS Biology:

Many OSW swimmers have no known ancestor that swam with median/paired fins, and the 22 species in this analysis belong toeight clades (groups of organisms stemming from a common ancestor). This suggests that the OSW evolved independently at least eight times. [Emphasis added.]

Casey Luskin has argued that Darwinians appeal to convergence in order to have it both ways: basically, "biological similarity implies common ancestry, except when it doesn't." The authors of this new paper do not respond to that charge specifically, but they go further than most Darwinians by not just asserting convergence occurred, but by offering evolutionary mechanisms that might produce it. They begin with broad philosophical questions:

How would life look if it evolved again on Earth, or for that matter, on any other habitable planet? The question of the role of chance versus necessity in evolution is a foundational issue in biology. Gould gave us the metaphor of the "tape of life" for the evolution of life and argued that if it were somehow rewound and started again, life would have taken a very different course. Conway Morris has argued that, on the contrary, the laws of physics limit the number of good solutions that are within reach of evolution, and that therefore we should expect life to take a similar course upon rewinding. Examples of convergent evolution, such as wings on insects, birds, and mammals, are considered supporting evidence for this hypothesis.But our understanding of convergent evolution, as reflecting the dominance of natural selection plus variation over factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, and other stochastic processes, is held back by a lack of quantitative arguments. Such arguments would expose the links from physical principles to the biological phenomena and help us understand where evolution is likely to converge to the same result or diverge to a wide variety of solutions.

Here, we present just such arguments for a phenomenon that unifies a vast diversity of swimming organisms, from invertebrates, like cuttlefish, to vertebrates, like cartilaginous and bony fish. Unlike the case of the convergently evolved wing, a morphological feature, here the evolved feature is a pattern of movement that occurs across a morphologically diverse set of moving appendages on aquatic animals.

We see at once that the implications go far beyond the knifefish's OSW. Evolutionary theory itself is at stake: Is it truly contingent, or somehow directed? Their argument hinges on the ability of the environment (e.g., the properties of water) to direct natural selection so that it rewards, with higher fitness, the animals that hit the optimum. If the OSW is on a peak of the fitness landscape, natural selection will drive an animal up the peak, no matter its ancestry, because it will outcompete the others. That's how separately evolving animals will end up (converge) on the same fitness peak.

What is the mechanism for macroevolutionary repeatability? In the language of the calculus of variations, these examples of convergent evolution -- if correctly identified as such -- imply that there is agradient in the fitness landscape toward some optimum with respect to trait in question, and this gradient is large enough to overcome competing factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, cases where optimality in one trait results in suboptimality in another trait ... and approximations of the trait which provide local but not global optimality. With a sufficiently steep gradient in fitness in place and evolutionary dynamics capable of achieving near-optimal solutions, it is only a matter of time before the mechanism of selection with variation can arrive at the optimum. As the derivative of the trait with respect to fitness is stabilizing,departures from the optimum would be self-correcting over evolutionary time.

In fulfillment of the promise of quantifying their argument, they measure the loss in force for wavelengths that deviate significantly from the OSW. "The effect of any decline in propulsive force -- even less than one percent -- from what it is at the OSW is amplified over the vast number of undulations an animal may make in its life," they argue. What animal would want to compete with less than the best?

Unfortunately, undulating fins are not the best. Tuna are the fastest swimmers in the ocean, but they rely on their caudal fins to thrust their bodies forward. So we have a conundrum; "The question is therefore why the slower forms of swimming exhibited by median/paired fin animals would emerge and thrivedespite the prevalence of body/caudal fin swimming in ancestral species." Why would evolution switch from the Ferrari to the Volkswagen?

The authors are ready with auxiliary hypotheses:

A similar question has arisen in simulation studies that show that alight-sensitive patch of skin can evolve through several intermediate forms into an advanced camera-type lens eye in only a few hundred thousand years -- why, then, are there so many existing animals with intermediate forms of eyes? Nilsson and Pelger's answer is that camera-type lens eyes are only the best solution for certain animal -- ecosystem combinations. Our answer is similar: body/caudal fin swimming makes little sense in isolation. It is only within particular ecological contexts that some types of animals are able to survive better with this type of swimming than with alternative approaches.

In particular, median/paired fin swimming appears to be a low speed, low cost of transport specialization. The lower amplitudes of fin movement that are possible in median/paired fin swimmers, compared to the very high amplitudes possible when the high power axial musculature is used in body/caudal fin swimmers, is thereforean advantage instead of a liability due to the lower energetic cost of transport of median/paired fin swimming. The fact that median/paired fin swimming is used at lower speeds should not be confused, however, with the concept of maximizing speed by swimming at the OSW. Even when swimming at lower speeds (or whatever speed for that matter, which is determined by frequency and amplitude), for a given set of parameters (amplitude of undulations, frequency, fin height, and fin shape), if an animal swims with elongated median/paired fins, then its speed can be maximizedfor that set of parameters by swimming at the OSW.

Our regular readers will jump at that lateral pass to Nilsson and Pelger. Their claim about the evolution of camera eyes was thoroughly trounced by David Berlinski almost a decade ago in these pages. It's an example of how scientists can continue to trust flawed arguments for years -- decades, sometimes -- without considering (or even knowing about) the counter-arguments.

Aside from that, the authors make a point: You can't just look at a fin in isolation. You need to consider the ecological niche of the animal. They point to members of the group Gymnotiformes, electric fish who use their ribbon fins in low-oxygen murky waters, that swim mostly at night where high speed is not advantageous.

Given these constraints, the elongated fins that are universally present within the more than 150 species comprising Gymnotiformesmay be favored, but clearly a tremendous amount of work would need to be done to assess the relative importance of all of these factors in giving rise to this one group of median/paired fin swimmers.

While the existence of body/caudal fin swimmers and the existence of median/paired fin swimmers may or may not be subject to robust repeatability, what is clear is that if median/paired fin swimming with elongated fins and semirigid trunks emerges -- as it has independently on multiple occasions according to Fig 1 -- it is very probable that the specific trait of swimming at the OSW will also emerge.

This is a very different claim, much reduced from the original one. No longer are they asserting that the environment will force different swimmers up the same fitness peak, because clearly it didn't for the tuna. Now we have the more modest claim that "if" a ribbon fin "emerges," then natural selection will push it toward the OSW. But where is their scientific law of emergence? What about the ocean environment can cause that? And we see they just admitted that their hypothesis "may or may not be subject to robust repeatability."

Another complication is that some of the undulating-fin fish can switch to high-speed caudal-fin swimming when needed, as when under attack from predators or when zooming in on prey. Why would natural selection provide both methods of propulsion? The fitness landscape just got more complicated; the animal has to climb multiple fitness peaks to survive. (We might point out, in passing, that according to evolutionists, electric organs are examples of convergence, too, having evolved six times independently according to a report last year from the University of Wisconsin posted at NewsWise.)

Notice, also, that while the ecological hypothesis seems to work for the Gymnotiformes, it doesn't for the others. Rays and cuttlefish, for instance, use their undulating fins in the open sea or coastal shallows during the daytime. The authors have not shown that their auxiliary hypotheses rescue convergent evolution, nor have they identified any evolutionary mechanism to account for fast swimmers with caudal fins swimming right alongside slow swimmers with undulating fins in the exact same watery environment. Every proposal has exceptions; where is that quantitative argument, exactly?

Thus, we can only speculate that the 7.5% decline in force occurring over the observed variation in SW is not large enough to overcomethe many causes of suboptimality listed above, whereas the 25% decline we find beyond this range is large enough to cause selection pressure toward the OSW. Additional research is needed to establish whether this hypothesis is true.

We thus circle back to Casey Luskin's challenge: Common ancestry explains traits, except when it doesn't.

For these reasons, we cannot take Robin Meadows's praise of this paper seriously:

This elegant work reveals that a physical problem -- how to get from here to there -- can be optimized by a wondrous diversity of biological solutions. Moreover, these findings strengthen the case thatmechanical optimization can drive evolution, contributing to the longstanding debate over the evolutionary roles of randomness versus physical constraints that limit the solutions that are feasible in living creatures. As the researchers point out, quantifying physical properties that underlie biological phenomena could help us recognize when an optimal mechanical solution is likely to drive convergent evolution.

Ockham is tapping his foot by the door.e knifefish, rather than having several fins like a trout, has one long "ribbon fin" that undulates along the length of its body. Studies of its motion reveal that it uses the optimal wavelength to get the most forward thrust, stability, and maneuverability out of its investment of energy. But the knifefish is not alone: the same optimal design can be found in cuttlefish (cephalopods), rays (cartilaginous fish), certain flatworms, and other bony fish that are evolutionarily unrelated. In fact -- if evolution by natural selection is assumed to be the cause -- this design emerged independently at least eight times. To the Darwinian, it's another remarkable case of "convergent evolution."

A paper in PLOS Biology investigates this phenomenon and tries to explain it. The five authors, primarily from Northwestern University, used a robotic knifefish to nail down the physical factors related to optimal swimming design: the length of the fin's undulation and the mean amplitude. Dividing the one by the other yields what they call the Optimal Specific Wavelength (OSW). Then they measured the OSW on 22 live swimmers, such as cuttlefish and rays, to see how they rated. They found that the values "converge to a narrow range" around 20, even though the animals belong to eight separate groups whose presumed ancestors did not possess this kind of propulsion. Robin Meadows says in a companion piece likewise in PLOS Biology:

Many OSW swimmers have no known ancestor that swam with median/paired fins, and the 22 species in this analysis belong toeight clades (groups of organisms stemming from a common ancestor). This suggests that the OSW evolved independently at least eight times. [Emphasis added.]

Casey Luskin has argued that Darwinians appeal to convergence in order to have it both ways: basically, "biological similarity implies common ancestry, except when it doesn't." The authors of this new paper do not respond to that charge specifically, but they go further than most Darwinians by not just asserting convergence occurred, but by offering evolutionary mechanisms that might produce it. They begin with broad philosophical questions:

How would life look if it evolved again on Earth, or for that matter, on any other habitable planet? The question of the role of chance versus necessity in evolution is a foundational issue in biology. Gould gave us the metaphor of the "tape of life" for the evolution of life and argued that if it were somehow rewound and started again, life would have taken a very different course. Conway Morris has argued that, on the contrary, the laws of physics limit the number of good solutions that are within reach of evolution, and that therefore we should expect life to take a similar course upon rewinding. Examples of convergent evolution, such as wings on insects, birds, and mammals, are considered supporting evidence for this hypothesis.But our understanding of convergent evolution, as reflecting the dominance of natural selection plus variation over factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, and other stochastic processes, is held back by a lack of quantitative arguments. Such arguments would expose the links from physical principles to the biological phenomena and help us understand where evolution is likely to converge to the same result or diverge to a wide variety of solutions.

Here, we present just such arguments for a phenomenon that unifies a vast diversity of swimming organisms, from invertebrates, like cuttlefish, to vertebrates, like cartilaginous and bony fish. Unlike the case of the convergently evolved wing, a morphological feature, here the evolved feature is a pattern of movement that occurs across a morphologically diverse set of moving appendages on aquatic animals.

We see at once that the implications go far beyond the knifefish's OSW. Evolutionary theory itself is at stake: Is it truly contingent, or somehow directed? Their argument hinges on the ability of the environment (e.g., the properties of water) to direct natural selection so that it rewards, with higher fitness, the animals that hit the optimum. If the OSW is on a peak of the fitness landscape, natural selection will drive an animal up the peak, no matter its ancestry, because it will outcompete the others. That's how separately evolving animals will end up (converge) on the same fitness peak.

What is the mechanism for macroevolutionary repeatability? In the language of the calculus of variations, these examples of convergent evolution -- if correctly identified as such -- imply that there is agradient in the fitness landscape toward some optimum with respect to trait in question, and this gradient is large enough to overcome competing factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, cases where optimality in one trait results in suboptimality in another trait ... and approximations of the trait which provide local but not global optimality. With a sufficiently steep gradient in fitness in place and evolutionary dynamics capable of achieving near-optimal solutions, it is only a matter of time before the mechanism of selection with variation can arrive at the optimum. As the derivative of the trait with respect to fitness is stabilizing,departures from the optimum would be self-correcting over evolutionary time.

In fulfillment of the promise of quantifying their argument, they measure the loss in force for wavelengths that deviate significantly from the OSW. "The effect of any decline in propulsive force -- even less than one percent -- from what it is at the OSW is amplified over the vast number of undulations an animal may make in its life," they argue. What animal would want to compete with less than the best?

Unfortunately, undulating fins are not the best. Tuna are the fastest swimmers in the ocean, but they rely on their caudal fins to thrust their bodies forward. So we have a conundrum; "The question is therefore why the slower forms of swimming exhibited by median/paired fin animals would emerge and thrivedespite the prevalence of body/caudal fin swimming in ancestral species." Why would evolution switch from the Ferrari to the Volkswagen?

The authors are ready with auxiliary hypotheses:

A similar question has arisen in simulation studies that show that alight-sensitive patch of skin can evolve through several intermediate forms into an advanced camera-type lens eye in only a few hundred thousand years -- why, then, are there so many existing animals with intermediate forms of eyes? Nilsson and Pelger's answer is that camera-type lens eyes are only the best solution for certain animal -- ecosystem combinations. Our answer is similar: body/caudal fin swimming makes little sense in isolation. It is only within particular ecological contexts that some types of animals are able to survive better with this type of swimming than with alternative approaches.

In particular, median/paired fin swimming appears to be a low speed, low cost of transport specialization. The lower amplitudes of fin movement that are possible in median/paired fin swimmers, compared to the very high amplitudes possible when the high power axial musculature is used in body/caudal fin swimmers, is thereforean advantage instead of a liability due to the lower energetic cost of transport of median/paired fin swimming. The fact that median/paired fin swimming is used at lower speeds should not be confused, however, with the concept of maximizing speed by swimming at the OSW. Even when swimming at lower speeds (or whatever speed for that matter, which is determined by frequency and amplitude), for a given set of parameters (amplitude of undulations, frequency, fin height, and fin shape), if an animal swims with elongated median/paired fins, then its speed can be maximizedfor that set of parameters by swimming at the OSW.

Our regular readers will jump at that lateral pass to Nilsson and Pelger. Their claim about the evolution of camera eyes was thoroughly trounced by David Berlinski almost a decade ago in these pages. It's an example of how scientists can continue to trust flawed arguments for years -- decades, sometimes -- without considering (or even knowing about) the counter-arguments.

Aside from that, the authors make a point: You can't just look at a fin in isolation. You need to consider the ecological niche of the animal. They point to members of the group Gymnotiformes, electric fish who use their ribbon fins in low-oxygen murky waters, that swim mostly at night where high speed is not advantageous.

Given these constraints, the elongated fins that are universally present within the more than 150 species comprising Gymnotiformesmay be favored, but clearly a tremendous amount of work would need to be done to assess the relative importance of all of these factors in giving rise to this one group of median/paired fin swimmers.

While the existence of body/caudal fin swimmers and the existence of median/paired fin swimmers may or may not be subject to robust repeatability, what is clear is that if median/paired fin swimming with elongated fins and semirigid trunks emerges -- as it has independently on multiple occasions according to Fig 1 -- it is very probable that the specific trait of swimming at the OSW will also emerge.

This is a very different claim, much reduced from the original one. No longer are they asserting that the environment will force different swimmers up the same fitness peak, because clearly it didn't for the tuna. Now we have the more modest claim that "if" a ribbon fin "emerges," then natural selection will push it toward the OSW. But where is their scientific law of emergence? What about the ocean environment can cause that? And we see they just admitted that their hypothesis "may or may not be subject to robust repeatability."

Another complication is that some of the undulating-fin fish can switch to high-speed caudal-fin swimming when needed, as when under attack from predators or when zooming in on prey. Why would natural selection provide both methods of propulsion? The fitness landscape just got more complicated; the animal has to climb multiple fitness peaks to survive. (We might point out, in passing, that according to evolutionists, electric organs are examples of convergence, too, having evolved six times independently according to a report last year from the University of Wisconsin posted at NewsWise.)

Notice, also, that while the ecological hypothesis seems to work for the Gymnotiformes, it doesn't for the others. Rays and cuttlefish, for instance, use their undulating fins in the open sea or coastal shallows during the daytime. The authors have not shown that their auxiliary hypotheses rescue convergent evolution, nor have they identified any evolutionary mechanism to account for fast swimmers with caudal fins swimming right alongside slow swimmers with undulating fins in the exact same watery environment. Every proposal has exceptions; where is that quantitative argument, exactly?

Thus, we can only speculate that the 7.5% decline in force occurring over the observed variation in SW is not large enough to overcomethe many causes of suboptimality listed above, whereas the 25% decline we find beyond this range is large enough to cause selection pressure toward the OSW. Additional research is needed to establish whether this hypothesis is true.

We thus circle back to Casey Luskin's challenge: Common ancestry explains traits, except when it doesn't.

For these reasons, we cannot take Robin Meadows's praise of this paper seriously:

This elegant work reveals that a physical problem -- how to get from here to there -- can be optimized by a wondrous diversity of biological solutions. Moreover, these findings strengthen the case thatmechanical optimization can drive evolution, contributing to the longstanding debate over the evolutionary roles of randomness versus physical constraints that limit the solutions that are feasible in living creatures. As the researchers point out, quantifying physical properties that underlie biological phenomena could help us recognize when an optimal mechanical solution is likely to drive convergent evolution.

Ockham is tapping his foot by the door.

From trash to treasure,no thanks to Darwinism

Junk No Mo: Scientists Turn Genetic Junk into Master Controller

Evolution News & Views May 8, 2015 2:45 PM 

You'll pardon two Aussies for their mixed metaphors. They represent the cutting edge of young scientists who have ditched the "junk DNA" label entirely. They now recognize the powerful regulatory role of micro-RNAs in the non-coding portions of the genome. Writing at The Conversation, Pamela Ajuyah (PhD student) and Nham Tran (lab head) at the University of Technology in Sydney begin their metaphors with a familiar irritation: junk mail.

Up until about two decades ago, one type of RNA, called microRNA, or just miRNA -- by virtue of them being very short, only 18-25 letters long -- were thought to be the junk mail of the genome, with no biological function. But today we know that these miRNA are actually not junk but play a very important role in regulating the activity of other parts of your DNA. [Emphasis added.]

After reviewing a little history about the Central Dogma and the Human Genome Project, they recount the surprise that only 2 percent of the human genome codes for proteins. "So the question is: what does the remaining 98 percent of our DNA actually do?" That's the spirit; seek function, and ye shall find. Biologists had made a big mistake by filtering the 98 percent into the spam folder.

For biologists, those important emails that slipped into the junk mail folder and were disregarded were miRNAs. That was until the first functional miRNA, lin-4, was officially discovered in 1993. Scientists were looking at the development of the nematode worm, Caenorhabditis elegans, and found that lin-4 inhibited protein synthesis of the lin-14 gene.

They subsequently found that miRNA can physically bind to mRNA and stop it creating proteins. Thus it effectively suppresses the activity of a gene. This discovery was thefirst evidence of miRNA negatively regulating RNA coding for proteins.

So, it turns out that the 98% of our genome that was regarded as "junk" might have a function after all.

After a little more history, catching up to the current count of 1,800 known functional miRNAs, they switch metaphors:

We now understand that miRNA control numerous genes and processes vital for cellular life such as metabolism, development and the immune system.

While two decades ago genes and proteins were seen as the most important players in what happens in our body, miRNAs are now recognised as the puppet masters, pulling the strings of various genes on the molecular biology stage.

Ajuyah and Tran appear genuinely excited about the prospects for discovering more function in the junk email (or more strings for the puppet master to pull). They talk about how cancerous tumors sometimes switch off the miRNAs that would otherwise activate anti-tumor proteins. This provides avenues for designing miRNAs to target tumors. Since miRNAs latch onto messenger RNAs promiscuously, it might allow miRNA-based drugs to target multiple genes simultaneously.

Back to the email analogy, they conclude:The interest in miRNA in the scientific community has increased exponentially in the last few years as researchers join in the race to develop a functional and effective miRNA-based therapeutic for cancer.

Far from being junk mail, miRNAs are the commands that redirect other messages, enabling some activities to go ahead and others to cease entirely. And now that biologists have updated their filters, they're now coming to grips with how powerful miRNAs can be.

We don't mind if the "puppet master" sets the "email filters" as long as everyone gets the message that the junk-DNA label belongs in the rear view mirror. (Mixing metaphors is addictive, isn't it?) What's going on here is one of the biggest paradigm reversals in decades: discovering that the junk is the master. Intelligent design theory expected that unknowns would prove functional. One only wonders how much further along genetics would be if the expectation of design had guided research two decades ago.

More Micro-RNA Function

A paper in Science, meanwhile, finds another function for miRNA: silencing the noisy genome. Hofman and Pilpel describe that discovery, then extend it into the search for additional functions of non-coding DNA:

And the story need not end with miRNAs. A most profound revolution in genomicsis the realization that there are many additional types of RNA. For instance,"antisense" RNAs may also act in noise filtration, especially when coregulated with their corresponding sense transcript. Perhaps some long noncoding RNAs, too, contribute to fine tuning of gene expression programs.

The Discarded Imagery

More evidence for the paradigm shift is seen in a review by Nathaniel Comfort in Nature of three new genetics books (including one, by Nessa Carey, reviewed by Casey Luskin here last week). His title is, "We are the 98 percent":

Today, junk DNA is at the heart of the most radical transformation of how we understand the genome since the information metaphor. Three books -- The Deeper Genome by John Parrington, Junk DNA by Nessa Carey, and Biocode by Dawn Field and Neil Davies -- present a vision of the twenty-first-century genome. Their relative success hinges on metaphor and imagery, both in how they conceive the genome and in the writing itself.

It's time for new metaphors, Comfort says; the encyclopedia image of the Central Dogma proved too static, the junk-DNA metaphor too limiting. He's not ready to believe all the non-coding regions are functional, but both metaphors (instruction book of life versus junk DNA) are outdated. "The old metaphor [instruction book] is not wrong; it is incomplete," he explains. "In theFinding apt imagery to replace the dead metaphor of the 'instruction book of life' could enable us to break free of the cliché of nature versus nurture. It could usher in a more democratic conception of life, in which all the world's a cell, and all the genes and genomes merely players.

That's a bit weird, but at least it's not dismissive of the genome as mostly junk. These are dynamic times as scientists revise old notions of the genome and try to visualize its complex functions. It appears that the concept of "junk DNA" itself is the thing most likely to end up on the junk pile. new genome, lines of static code have become a three-dimensional tangle of vital string, constantly folding and rearranging itself, responsive to outside input."

So what should be the new metaphor to describe a genome that is "more than a set of rules and parts descriptions"?

On Mathematics and darwinism.

Mathematicians and Evolution

As recently highlighted here, mathematics is an academic locale where scientific skepticism of Neo-Darwinism can survive the current political climate! Discovery Institute recently received an e-mail from someone commenting on the Scientific Dissent from Darwinism List where over 600 Ph.D. scientists from various fields agree that they are "skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life." This skeptic of evolutionary-skepticism e-mailer wrote "I'm a mathematician and certainly am NOT qualified to support such a statement. Only evolutionary biologists are qualified to respond here." While the Dissent from Darwinism list does contain individuals trained in evolutionary biology, the question remains "Is the objection valid?"

The truth is that mathematics has a strong tradition of giving cogent critique of evolutionary biology. After all, Darwin's theory of evolution by natural selection is fundamentally based upon an algorithm which uses a mathematically describable trial and error process to attempt to produce complexity. Population genetics is rife with mathematics. In fact, one criticism of the alleged transitional fossil sequences for whales is that they represent evolutionary change on too rapid a timescale to be mathematically feasible. It seems that there is no good reason why those trained in mathematics cannot comment on the ability of the Neo-Darwinian mutation-selection process to generate the complexity of life.

One of the best known mathematical forays into evolution was the 1966 Wistar Symposium, held in Philadelphia, where mathematicians and other scientists from related fields congregated to assess whether Neo-Darwinism is mathematically feasible. The conference was chaired by Nobel Laureate Sir Peter Medawar. The general consensus of many meeting participants was that Neo-Darwinism was simply not mathematically tenable.  

The proceedings of that conference, Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), reports various challenges to evolution presented by respected mathematicians and similar scholars at the conference. For example, the conference chair Sir Peter Medawar stated at the outset:

"[T]he immediate cause of this conference is a pretty widespread sense of dissatisfaction about what has come to be thought as the accepted evolutionary theory in the English-speaking world, the so-called neo-Darwinian Theory. ... There are objections made by fellow scientists who feel that, in the current theory, something is missing ... These objections to current neo-Darwinian theory are very widely held among biologists generally; and we must on no account, I think, make light of them. The very fact that we are having this conference is evidence that we are not making light of them."

(Sir Peter Medawar, "Remarks by the Chairman," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. xi, emphasis in original)

Various scientists, including some mathematicians, proceeded to comment about problems with Neo-Darwinism:

"[A]n opposite way to look at the genotype is as a generative algorithm and not as a blue-print; a sort of carefully spelled out and foolproof recipe for producing a living organism of the right kind if the environment in which it develops is a proper one. Assuming this to be so, the algorithm must be written in some abstract language. Molecular biology may well have provided us with the alphabet of this language, but it is a long step from the alphabet to understanding a language. Nevertheless a language has to have rules, and these are the strongest constraints on the set of possible messages. No currently existing formal language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed. Any changes must be syntactically lawful ones. I would conjecture that what one might call "genetic grammaticality" has a deterministic explanation and does not owe its stability to selection pressure acting on random variation."

(Murray Eden, "Inadequacies as a Scientific Theory," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. 11)

"[I]t seems to require many thousands, perhaps millions, of successive mutations to produce even the easiest complexity we see in life now. It appears, naively at least, that no matter how large the probability of a single mutation is, should it be even as great as one-half, you would get this probability raised to a millionth power, which is so very close to zero that the chances of such a chain seem to be practically non-existent."

(Stanislaw M. Ulam, "How to Formulate Mathematically Problems of Rate of Evolution," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. 21)

"We do not know any general principle which would explain how to match blueprints viewed as typographic objects and the things they are supposed to control. The only example we have of such a situation (apart from the evolution of life itself) is the attempt to build self-adapting programs by workers in the field of artificial intelligence. Their experience is quite conclusive to most of the observers: without some built-in matching, nothing interesting can occur. Thus, to conclude, we believe that there is a considerable gap in the neo-Darwinian theory of evolution, and we believe this gap to be of such a nature that it cannot be bridged within the current conception of biology."

(Marcel Schutzenberger, "Algorithms and Neo-Darwinian Theory," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. 75)

These are potent arguments from academics qualified to assess the mathematical ability of a random / selective process to produce complexity. While evolutionary biologists and other types of biologists can yield many insights into evolutionary biology, scientists other than biologists, such as mathematicians, are most certainly qualified to comment on the feasibility of Neo-Darwinian evolution.

On Darwinian hagiography

Scientific Consensus? You've Got to Be Kidding, Right?

Evolution News & Views May 4, 2015 3:51 AM | 

We are often told that "nothing in biology makes sense except in the light of evolution." The statement was first made in 1973 by neo-Darwinist Theodosius Dobzhansky. (Neo-Darwinism is the view that evolution is due to the natural selection of variations that originate as gene mutations.) Dobzhansky's statement is false. Nevertheless, it has become the majority opinion ("consensus") of the scientific establishment. Sometimes, it is carried to absurd extremes.

For example, in a blog post last week defending that reliability of "scientific consensus," theoretical astrophysicist Ethan Siegel wrote:

[E]volution was the consensus position that led to the discovery of genetics...

What a hoot! The truth is that Gregor Mendel discovered genetics with no help from evolution. Mendel published his theory about the same time that Charles Darwin published The Origin of Species, but Mendel did not accept Darwin's theory, and Darwin's followers ignored Mendel's theory for decades.

Here's an excerpt from a chapter titled "You'd Think Darwin Invented the Internet" in Jonathan Wells's book, The Politically Incorrect Guide to Darwinism and Intelligent Design:

Augustinian monk Gregor Mendel found Darwin's theoryunpersuasive. The data he collected led him to conclude that heredity involves the transmission of stable factors that determine an organism's traits. Although the factors can be mixed and matched during reproduction, they remain discrete and unchanging from one generation to the next. Darwin's view of heredity was quite different. He believed that every cell in an organism produces "gemmules" that transmit characteristics to the next generation in a blending process he called "pangenesis." The advantage of Darwin's view was that gemmules could be changed by external conditions, or by use and disuse, and thus account for evolutionary change. The disadvantage of Darwin's view was that it was false.

Mendel's theory of stable factors contradicted Darwin's theory of changeable gemmules. Thus, although Mendel's work was published in 1866, Darwinists totally ignored it for more than three decades. William Bateson, one of the scientists who "rediscovered" Mendelian genetics at the turn of the century, wrote that the cause for this lack of interest was "unquestionably to be found in that neglect of the experimental study of the problem of Species which supervened on the general acceptance of the Darwinian doctrines... The question, it was imagined, had been answered and the debate ended."

Even after 1900, Darwinists had little use for Mendel's theory. By the 1930s, however, the evidence had corroborated Mendelian genetics. Darwinists abandoned pangenesis and subsumed Mendelism in a "neo-Darwinian synthesis" that still dominates evolutionary biology.

In 1999, Darwinist Bruce Alberts claimed that Darwinism is "at the core of genetics." Yet Mendel had no need for Darwin's hypothesis. How can Darwinism, which contributed nothing to the origin of genetics and resisted it for half a century, now be at its core? It is Darwinism that needs genetics, not genetics that needs Darwinism.

Of course, the "scientific consensus" now holds that Darwinian evolution is true, and the main point of Siegel's blog post is to argue for the trustworthiness of the "scientific consensus." But Siegel makes it clear that most people don't count as scientists:

In order to become and remain a scientist, you need a four-year degree with a major in your chosen scientific field, a four-to-six-year (on average) PhD degree, where you specialized in a particular sub-field of your science and demonstrated yourself capable of making original contributions, and continued to remain active in the field, staying abreast and even participating in many of the latest discoveries.

The skills you develop as a scientist are unique to scientists, and the ability to interpret results in the context of your sub-field and what's known about it is unique to scientists within that sub-field.

And finally -- and this is the most important part -- in order to obtain an accurate, nuanced, complete picture of a particular problem or set of problems, you need this incredible set of scientific knowledge and experience that is (in most cases) non-transferrable from one discipline to another.

Whoa! By these criteria, Siegel should stick to his own specialty, theoretical astrophysics. He should leave biology to biologists, such as Jonathan Wells(PhD in Molecular and Cell Biology, University of California at Berkeley).

But here's the catch: Jonathan Wells is not part of the "scientific consensus" in biology, because he doesn't accept Darwinian evolution. Of course, Gregor Mendel was not part of the "scientific consensus" in his day. In fact, not even Charles Darwin became part of the "scientific consensus" until his theory was propped up by Mendelian genetics almost half a century later.

So what are we to make of the "scientific consensus" about evolution? Probably no one can say it better than David Berlinski, who wrote in The Devil's Delusion:

Within the English-speaking world, Darwin's theory of evolution remains the only scientific theory to be widely championed by the scientific community and widely disbelieved by everyone else. No matter the effort made by biologists, the thing continues to elicit the same reaction it has always elicited: You've got to be kidding, right?

And now the good news.

THE WATCHTOWER MAY 2015

 COVER SUBJECT | IS THE END NEAR?

“The End”—What Does it Mean?

hen you hear the words “The end is near!” what comes to mind? Do you think of a wild-eyed preacher thundering from the pulpit and gesturing dramatically, Bible in hand? Or do you picture a bearded old man standing on a street corner, wearing a long robe tied at the waist with a rope, holding a sign bearing a doomsday message? Imagining such scenes may make some people feel concerned, while others may feel skeptical or even amused.

The Bible does state: “The end will come.” (Matthew 24:14) The same event is also called “the great day of God” and “Armageddon.” (Revelation 16:14, 16) True, there is much religious confusion on the subject and strange, gloomy notions abound. Nonetheless, the Bible itself is quite clear about the end—revealing what it is and what it is not. God’s Word also helps us to see clearly whether the end is near. Best of all, it teaches us how to survive! First, though, let us clear up some misconceptions and establish a definition. What does “the end” really mean according to the Bible?

 WHAT THE END IS NOT

1. THE END IS NOT AN EPIC, FLAMING DESTRUCTION OF THE EARTH.
   The Bible states: “[God] has established the earth on its foundations; it will not be moved from its place forever and ever.” (Psalm 104:5) That scripture and others assure us that God will neither destroy the earth nor allow it to be destroyed—ever!—Ecclesiastes 1:4; Isaiah 45:18.
2. THE END IS NOT A RANDOM, UNSCHEDULED EVENT.
   The Bible reveals that the end is scheduled—God has set a specific time for it. We read: “Concerning that day or the hour nobody knows, neither the angels in heaven nor the Son, but the Father. Keep looking, keep awake, for you do not know when the appointed time is.” (Mark 13:32, 33) Clearly, God (“the Father”) has scheduled the exact “appointed time” when he will initiate the end.
3. THE END IS NOT TRIGGERED BY HUMANS OR BY DEBRIS HURTLING THROUGH SPACE.
   What will bring about the end? Revelation 19:11 says: “I saw heaven opened, and look! a white horse. And the one seated on it is called Faithful and True.” Verse 19 continues: “And I saw the wild beast and the kings of the earth and their armies gathered together to wage war against the one seated on the horse and against his army.” (Revelation 19:11-21) Though much of the language here is symbolic, we can readily discern this much: God will send an army of angelic creatures to exterminate his enemies.

The Bible’s message about the end is good news rather than bad

WHAT THE END IS

1. THE END OF FAILING HUMAN GOVERNMENTS.
   The Bible explains: “The God of heaven will set up a kingdom [government] that will never be destroyed. And this kingdom will not be passed  on to any other people. It will crush and put an end to all these kingdoms, and it alone will stand forever.” (Daniel 2:44) As was stated earlier, in point 3, there will be an extermination of “the kings of the earth and their armies,” who will have “gathered together to wage war against the one seated on the horse and against his army.”—Revelation 19:19.
2. THE END OF WAR, VIOLENCE, AND INJUSTICE.
   “[God] is bringing an end to wars throughout the earth.” (Psalm 46:9) “Only the upright will reside in the earth, and the blameless will remain in it. As for the wicked, they will be cut off from the earth, and the treacherous will be torn away from it.” (Proverbs 2:21, 22) “Look! I am making all things new.”—Revelation 21:4, 5.
3. THE END OF RELIGIONS THAT HAVE FAILED GOD AND HUMANS.
   “The prophets prophesy lies, and the priests dominate by their own authority. . . . But what will you do when the end comes?” (Jeremiah 5:31) “Many will say to me in that day: ‘Lord, Lord, did we not prophesy in your name, and expel demons in your name, and perform many powerful works in your name?’ And then I will declare to them: ‘I never knew you! Get away from me, you workers of lawlessness!’”—Matthew 7:21-23.
4. THE END OF PEOPLE WHO PERPETUATE AND SUPPORT THE CURRENT STATE OF AFFAIRS.
   Jesus Christ said: “Now this is the basis for judgment: that the light has come into the world, but men have loved the darkness rather than the light, for their works were wicked.” (John 3:19) The Bible describes an earlier worldwide destruction during the time of the faithful man Noah. “The world of that time suffered destruction when it was flooded with water. But by the same word the heavens and the earth that now exist are reserved for fire and are being kept until the day of judgment and of destruction of the ungodly people.”—2 Peter 3:5-7.

Note that the upcoming “day of judgment and of destruction” is compared with the destruction of “the world” of Noah’s time. What world was destroyed? Our planet survived; it was “the ungodly people”—God’s enemies—who “suffered destruction.” During God’s upcoming “day of judgment,” those who choose to be God’s enemies will likewise be destroyed. But God’s friends will be preserved, as were Noah and his family.—Matthew 24:37-42.

Imagine how splendid this earth will be after God eliminates all wicked influences! Clearly, the Bible’s message about the end is good news rather than bad. Still, you may wonder: ‘Does the Bible tell us when the end will come? Could it be near? How can I survive it?’

AFTER THE END

What will it be like after the end? Many scriptures describe that wonderful time. For example: “‘[God] will wipe out every tear from their eyes, and death will be no more, neither will mourning nor outcry nor pain be anymore. The former things have passed away.’ And the One seated on the throne said: ‘Look! I am making all things new.’” (Revelation 21:4, 5) The end does not have to mean the end of your life. God wants us to survive, and he tells us how.