#vicariance

godlike-and-cowering:

1) Darwin defined the mechanism of evolution as decent with modification, and what he hypothesized was a trend in the fossil record showing small changes into speciation. We don’t see that. Archeologists don’t see that. Paleontologists don’t see that. We see punctuated equilibrium. That’s the notion that species arise abruptly at sporadic points in time. Almost as if they might have been placed here? Ponder

I’ll set aside all of the Deepak Chopra-esque woo woo you talked about in our chat and focus on your egregious ignorance on evolution. Descent with modification is precisely what we see. It’s fine to be ignorant of the fossil record, but gradual changes do result in macroevolutionary speciation stemming beyond beak length and girth, fur pigmentation, neck size, and so on; I’ll go over this in detail later. I already discussed whale evolution and human evolution in a previous response. I briefly mentioned horse evolution, but that’s another marquee example of macroevolution:

This isn’t an example of punctuated equilibrium, which you misdefine as species arising abruptly because “they might have been placed there” – so I’ll return to that in a bit; this is an example of evolutionary modification over long periods of time resulting in speciation. Paleontologists have certainly seen what you said they don’t see. If not for being able to see what you’re claiming they’re blind to, we wouldn’t have such clear examples in the fossil record.

Before I go on, punctuated equilibrium is a hypothesis put forward by Stephen Jay Gould and Niles Eldridge, which states that even over a period of millions of years, species are stable. This much more gradual change is then punctuated by rapid changes resulting in new species. This change is then followed by further stability. Bryozoan have been stable for roughly 140 million years and their fossil record appears to confirm Gould and Eldridge’s hypothesis. As Berkley’s Evolution page tells us, however, punctuated equilibrium doesn’t:

- Suggest that Darwin’s theory of evolution by natural selection is wrong. - Mean that the central conclusion of evolutionary theory, that life is old and - organisms share a common ancestor, no longer holds. - Negate previous work on how evolution by natural selection works. - Imply that evolution only happens in rapid bursts.

Punctuated equilibrium isn’t a challenge to natural selection. It’s simply another evolutionary model and it isn’t at all clear that punctuated equilibrium occurs most frequently or that it is the dominant evolutionary model. That debate rages on, but there are of course cases that show it to be less prevalent. In fact, homologies and atavisms may show that punctuated equilibrium is uncommon. As Jerry Coyne explains:

The most striking atavism in our own species is called the “coccygeal projection,” better known as the human tail. As we’ll learn shortly, early in development human embryos have a sizable fishlike tail which begins to disappear about seven weeks into development (its bones and tissues are simply reabsorbed by the body). Rarely, however, it doesn’t regress completely, and a baby is born with a tail projecting from the base of its spine (figure 14). The tails vary tremendously:  some are “soft.” without bone, while others contain vertebrae — the same vertebrae normally fused together in our tailbone. Some tails are an inch long, others nearly a foot. And they aren’t just simple flaps of skin, but can have hair, muscles, blood vessels, and nerves. Some can even wiggle! Fortunately, these awkward protrusions are easily removed by surgeons.

What can this mean, other than that we still carry a developmental program for making tails? Indeed, recent genetic work has shown that we carry exactly the same genes that make tails in animals like mice, but these genes are normally deactivated in human fetuses. Tails appear to be true atavisms.

Coyne, Jerry A. Why evolution is true. Oxford: Oxford U Press, 2010. 65-66 Print.

What you miss and clearly didn’t anticipate as a part of my response is the genetic component. All phenotypical traits have corresponding genotypes. A phenotypical trait is what’s observed when genes are expressed whilst the genotype is what results in such traits. Without a clear understanding of the genotype-phenotype distinction, natural selection can’t be understood. I must add that while there is a clear distinction between the two, there’s also a clear causal connection and this is precisely what Coyne points out. We have tail-making genes, but generally speaking, humans don’t develop tails. That’s because the tail-making genes do not express themselves, hence there’s no corresponding phenotypical trait. When they do happen to express themselves, there’s a corresponding phenotypical trait.

For anyone who might be confused, an atavism is not a vestigial trait. The human tail is sometimes erroneously considered a vestigial trait, but it isn’t because it’s not a non-functioning version of a tail. In other words, if all humans were born with tails that don’t wiggle, wag, and so on, then it would be a lot more like an ostrich’s wings. The ostrich has repurposed its wings to help it maintain balance and to add thrust when it runs, but an ostrich notably doesn’t and cannot fly. Their wings are vestigial structures. 

Atavisms, on the other hand, are phenotypical traits that reappear in a modern individual or even within a genomic lineage but not in a population. It is entirely possible for a grandparent, parent, and child to have been born with a tail; this is an example of an atavism reappearing in a lineage. Though that’s possible, there are no observed instances of any large portion of the human population being born with tails. In any case, the tail, unlike the human appendix, is not a repurposed structure and thus, isn’t a vestigial trait.

Homologies may appear to show a so-called body plan by a designer in the minds of some, but homologies, if that view is to be taken seriously, show only a severe lack of imagination. As Francois Jacobs noted, evolution is a tinkerer. It isn’t at all like a designer and this is precisely why this apparent lack of imagination is widespread. As Prothero explains:

For example, the basic vertebrate forelimb has the same basic elements: a single large bone (the humerus), a pair of two long bones in the forearm (the radius and ulna), a number of wrist bones (carpals and metacarpals), and multiple bones (phalanges) support five digits (fingers). But look at the wide array of ways that some animals use this basic body plan! Whales have modified them into a flipper, while bats have extended the fingers out to support a wing membrane. Birds also developed a wing, but in an entirely different way, with most of the hand and wrist bones reduced or fused together, and feather shafts providing the wing support instead of fingers bones. Horses have lost their side toes and walk on one large finger, the middle finger. None of this makes any sense unless these animals inherited a standard body plan in place from their distinct ancestors and had to modify it to suit their present-day function and ecology. These common elements (bones, muscles, nerves) that serve different functions despite being built from the same basic parts are known as homologous structures. For example, the finger bones of a bat wing are homologous with our finger bones, and so on. 

Prothero, Donald R., and Carl Dennis. Buell. Evolution: what the fossils say and why it matters. New York: Columbia U Press, 2007. 105-106. Print.

He goes on to explain that an “intelligent designer” wouldn’t jury-rig these structures using the bones that these individuals inherited from their ancestors. Indeed a perfect and infinitely intelligent designer would design wings in the best way possible. Whale flippers wouldn’t have differed in their bone configuration compared to the flippers of fish and marine reptiles. Though all of these structures have the same function, all of them are configured differently, and though they’re configured differently, they are inherited from the organism’s ancestors. 

While you’re looking for justification in the fact that species arise rapidly “as though they were put there” or created from scratch, you’re paying attention to what’s on the surface. In other words, punctuated equilibrium cannot and doesn’t attempt to disprove the notion that structures like wings, flippers, and hands evolved, and that they evolved from ancestral bones. Speciation isn’t the only evidence we have; genotypes resulting in phenotypical traits aren’t the only evidence we have; we also have evidence of ancestral bone structures being reconfigured to suit modern purposes. If punctuated equilibrium were a challenge to natural selection, atavisms and homologies would be explained alternatively and better, or be explained away entirely; punctuated equilibrium doesn’t accomplish that.

2) two scientists tried and failed to propose a start to the central dogma of biology which is DNA -> RNA -> PROTEINS Even using ribozymes with amino acids and lighting in a shallow bed couldn’t assemble the right order or even close to a viable RNA transcript that could also self replicate. Even under water under pressures and thermal heat, still the same outcome. It’s a “what came first, the chicken or the egg?” Type of equation that still baffles EVERY BIOLOGIST TODAY. You need critical proteins to replicate or transcribe DNA or RNA, and those critical proteins are encoded in the RNA, which is encoded in the DNA. If this isn’t clear please let me know because I want to make sure you understand that this isn’t something any scientist can sidestep. Not now, so let future generations that have better answers use biology to undermine a common architect.

This is a classic example of an argument from ignorance or alternatively, an argument from personal incredulity. Falling short of saying your argument fails because it’s fallacious, which would constitute a fallacy on its own, namely fallacy fallacy, I’m going to point out that your whole argument is a fallacy. It’s as good as Hoyle’s Fallacy. You’re basically concluding that since past and modern scientists haven’t established abiogenesis, that future scientists can’t. That’s a fallacious inductive argument stemming from your desperate need to believe in a creator. There’s that and having the sequence entirely wrong. RNA World actually posits RNA (ribozymes) –> DNA –> Proteins. Ribozymes catalyzed chemical reactions in the earliest lifeforms. These reactions eventually resulted in DNA and more complex protein synthesis. 

Aside from that, you act as though abiogenesis is limited to RNA World. You say nothing of panspermia or what the Uray-Miller Experiment attempted to show, namely that life started with an electric spark. You also say nothing of the prevalence of hydrothermal vents in the oceans of ancient Earth, a place where chemosynthetic organisms are known to thrive. Panspermia is especially enticing given that the building blocks of life have been found on meteorites and that, in fact, the building blocks are ubiquitous not only in our solar system, but in the universe. Life here might have been seeded from elsewhere and far from pushing the buck back, it’s a matter of probability. 

What’s more probable – an invisible, incompetent designer making life from scratch or organic matter arising from inorganic matter? What’s more probable – an incompetent designer using organic matter to animate life or organic matter going through gradual chemical evolution and eventually resulting in life? The probability favors the idea that well-established inorganic to organic reactions eventually resulted in organic compounds resulting in life. RNA World is simply one way that might have happened, but certainly not the only way that’s been proposed. 

In any case, god used to be the widespread explanation for everything from storms to earthquakes to volcanic eruptions. Since these have been thoroughly explained without requiring supernatural agency, what’s next is to relegate god to what remains of human ignorance. Specifically, since we don’t yet know in full detail how the universe and life came to be, god is the placeholder explanation. Given your penchant for inductive arguments (faulty ones at that), I’ll present a much more compelling and likely inductive argument. 

This is where you point and laugh and say the predictable: “taking notes from a comedian…LOLz.” Well, it’s quite telling that a comedian, not a scientist, has a better grasp of reality than you do. He makes a valid point anyway and pointing out that he’s a comedian is ad hominem. Philosophy is a human endeavor and as such, everyone has the potential to do good philosophy – and here, Minchin is presenting a solid inductive argument and thus, doing good philosophy.

God or supernatural agents used to be a primary mode of explanation. That simply isn’t the case anymore. People like yourself have relegated god to the posts of our ignorance, but as history has shown time and again, the god explanation will be decisively supplanted by a better, more objective explanation. Moreover, that explanation will be replicable and falsifiable. The god explanation obviously lacks basic scientific criteria in that it isn’t replicable; it’s merely false consensus. It also isn’t falsifiable because apparently, even the notion of a multiverse doesn’t cancel out the god explanation for some believers. Believers don’t allow the god explanation to go away because they’re intransigent individuals who have a desperate, deeply rooted need to believe. 

They have projected their ego and psychological fragility onto the whole of the universe in stating that the creator must look like and favor them. Aside from that, the god explanation has been regressive and stagnating rather than progressive. The god explanation leads to no proliferation of knowledge, breakthroughs, and solutions. It leaves us completely and utterly without sound explanation for our current ignorance. There once existed a woo woo believer like you that said that scientists and natural philosophers will never figure out x or y; once they did figure out x or y, the matter became a and b; then they figured out a and b, and so the matter became w and x, and so on. “God is the ever-receding pocket of scientific ignorance”, as Neil deGrasse Tyson so wonderfully put it.

3) you must be thinking of micro evolution because that is something that biologists do all agree on. This is the notion that evolutionary changes can occur selectively within a species especially over a short period of time. This is the example of Darwin’s finches, and the break of the polar bears, all these examples I’m sure you would have hoped to fuck me with. Especially changes within the gene pool. But you would see that even polar bears and grizzleys would have a viable cub. You would see that darwin’s finches would be in fact fertile and viable. They’re the same species. There’s no speciation. What defines speciation across the board is the ability for two organisms to provide a viable fertile offspring. Would you call every dog a different species? When we can cross breed every one like we have for centuries? See, evolution is one species giving rise to many. We don’t even have a clean example of a definitive species giving rise to another completely. That’s macroevolution. That’s something the scientists of tomorrow also need to investigate to substantiate your take on evolution. So until then, hold those arguments also.

My “take” on evolution has already been firmly substantiated. Apart from the two fossil records I summarized in my response to that other evolution denier, I briefly went over another one above. Aside from that, I went over evolution at the genetic and phenotypical level, something you failed to anticipate. What’s more is that we do have clean examples of one species, over a long period of time, giving rise to a completely different species. In fact, the emergence of polar bears is a macroevolutionary example! All you show here is a misapprehension of evolution.

You don’t understand macroevolution. You’re not thinking one species branching off into two or more distinct species. You’re thinking pokemon; you’re thinking Dratini becoming Dragonite with one intermediary barely explaining how the thing went from a sea dragon to a bipedal dragon with wings! That’s not macroevolution. Dogs are, first and foremost, the product of mostly artificial selection and any difference in breeds is selected, directly or indirectly, by humans.

Macroevolution, on the other hand, has been observed repeatedly. You gave an example in the emergence of polar bears. There’s also the example of homo antercessor splitting into homo neaderthalensis and homo sapien, and perhaps even Denisovans, homo floresiensis and homo naledi. Whales, dolphins, and porpoises are cetaceans with a common ancestor and apart from the many distinct whale, dolphin, and porpoise species we have today, there are many that have gone extinct. Again (!), we have plenty of fossils. So pronounced is this macroevolutionary change, that the criterion of interbreeding is no longer met. A blue whale wouldn’t even attempt to breed with a say, an hourglass dolphin or a clymene. Heck, it wouldn’t even attempt breeding with a humpback or beluga. 

The issue with what you’re saying narrows down to scientific illiteracy. You limit speciation to sympatric speciation and utterly ignore allopatric speciation. What you describe, namely two species that are geographically close enough to interbreed, is sympatric speciation. What you don’t even mention is allopatric speciation, which occurs when species sharing a common ancestor are geographically isolated or vicariant and therefore, can’t breed. Vicariance prevents gene flow and therefore, interbreeding. As PBS explains:

An example of vicariance is the separation of marine creatures on either side of Central America when the Isthmus of Panama closed about 3 million years ago, creating a land bridge between North and South America. Nancy Knowlton of the Smithsonian Tropical Research Institute in Panama has been studying this geological event and its effects on populations of snapping shrimp. She and her colleagues found that shrimp on one side of the isthmus appeared almost identical to those on the other side – having once been members of the same population.

But when she put males and females from different sides of the isthmus together, they snapped aggressively instead of courting. They had become separate species, just as the theory would predict.

You also didn’t mention parapatric speciation. Though it occurs a much lesser frequency, it has been observed. Parapatric speciation is being observed, in real time, in Anthoxanthum odoratum. A portion of the species lives in contaminated soil and have developed tolerance for heavy metals whilst another portion lives in the same soil and has not developed this tolerance. The tolerant plants and intolerant plants are geographically near to one another and yet, they don’t fertilize with one another because their flowering times differ. We are observing, in real time, the permanent end to gene flow within a continuous population.

I strongly suggest that you get a handle on what you’re looking to deny before speaking on the matter. I promised not only to put your ignorance on display, but also to correct it – not so much for you, but for people who share your views. It is a known fact that the person receiving correction tends to double down. It is also known that minds are changed indirectly and in private. I’m not so much concerned about you correcting your ignorance; I don’t see that happening anytime soon because it appears your need to believe is tied to psychological changes resulting from frequent narcotics (ab)use. 

Exchanges like this do present good opportunity to communicate to them who are currently ignorant but have no stake in this particular game. My point isn’t to demean them, but rather to get them to understand that they don’t actually understand what they purport to understand and that, in fact, they lack even a perfunctory grasp of the topic. You don’t get evolution and that much is clear by a failure to understand the genotype-phenotype distinction and connection, the micro-macro distinction, and the types of speciation there are. Apart from that, you lack a basic comprehension of what constitutes a scientific theory, which explains why you think the god explanation holds water. You also show a lack of depth in the topic of abiogenesis, pretending to debase merely one theory (RNA World) whilst also demonstrating a poor understanding of the theory. 

Blog post about a recent paper I published on Ecography with Robert Boria and Robert Anderson.

I mean... there is. Obviously, all birds come from a common flying ancestor.

But I think what you mean is that you don't think that the ratites got to their current positions across the globe by flying to them and then independently losing the ability to fly? Rather, you prefer the notion that the flightlessness among ratites is a synapomorphy of the group, and they arrived at their current positions by rafting or simple continental drift?

That's the oldschool opinion, which most studies are now saying is wrong. But my thesis showed that not a single study produced so far gives an unambiguous answer to the question. Ultimately, until we find concrete missing link fossils, or sequence whole fossil genomes, we are not going to get an answer to the question.