Do patterns of phylogenesis show evolution?

[Difflugia]

Question for debate: Are the patterns seen in molecular phylogenies sufficient to show that biological evolution occurred?

For reference and easier Googling, the science of generating evolutionary trees is known as cladistics or phylogenetic systematics. Using DNA sequence data to generate the trees is molecular phylogeny.

The standard of evidence I'll be discussing is reasonable doubt. Even that's pretty broad, but if your argument hinges on "possible," you should be able to at least quantify that.

I've generated phylogenies using online tools previously and discussed them in this post. I tried to start a tutorial in this thread. If someone wants to discuss how to actually use the tools and data, feel free to ask questions in the tutorial thread and I'll pick it back up.

This debate question is a response to this comment.

[The Barbarian]

Scientific data can show the likelihood of a young earth but committed old earth specularists refuse to interpret the data that way.

AI Overview
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According to some creationist arguments, the low levels of helium in Earth's atmosphere suggest a young Earth, as the rate at which helium is produced from radioactive decay should result in a much higher concentration if the Earth were billions of years old; however, mainstream science rejects this claim, citing issues with the calculations used and the complex dynamics of atmospheric gas escape mechanisms.

Turns out, the escape of helium from the atmosphere is about what you'd expect, given the helium concentration in the atmosphere and the release of helium from the crust of the Earth:

Atmospheric helium is in dynamic equilibrium between the gain of helium diffusing from Earth's crust (as a product of radioactive decay) and losses of helium into space.
https://energy.utah.gov/wp-content/uplo ... Plan-1.pdf[/quote]

I expect that YE creationists honestly didn't realize how the system works; this is probably an error, not an intentional dishonesty. I've seen similar arguments concerning the amount of salt in the oceans. There's a dynamic equilibrium with that, also.

Of course there is always an alternative speculation to overturn obvious conclusions from scientific data that biased participants do not like.

YE creationists do not like the data showing that helium from radioactive breakdown in the Earth continues to replenish helium even as it continues to offgas into space. However, the facts are what they are, and so the "too much helium story" falls apart on inspection.

Since evolution kept regularly pushing back old age estimated timelines there came a point more than 100 year ago when evolutionists had to come up with a different source for the energy of the sun because gravitational contraction proposed by Lord Kelvin meant the sun was no older than 30 million years. The new theory was nuclear fusion which first emerged in 1920.

Turns out, nuclear fusion is a fact. That's what a hydrogen bomb does. Now we can produce nuclear fusion in controlled experiments; it's a promising source of energy, if we can increase the efficiency of the process a bit. No point in denying the fact.

There was a problem with the math and evidence,

In the case of the helium story, there was a problem with the evidence showing helium continuing to form and offgas from the Earth itself. In the words of Thomas Huxley, "a lovely little theory, killed by an ugly fact."

[marke]

Scientific data can show the likelihood of a young earth but committed old earth specularists refuse to interpret the data that way.

AI Overview
Learn more
According to some creationist arguments, the low levels of helium in Earth's atmosphere suggest a young Earth, as the rate at which helium is produced from radioactive decay should result in a much higher concentration if the Earth were billions of years old; however, mainstream science rejects this claim, citing issues with the calculations used and the complex dynamics of atmospheric gas escape mechanisms.

Turns out, the escape of helium from the atmosphere is about what you'd expect, given the helium concentration in the atmosphere and the release of helium from the crust of the Earth:

Atmospheric helium is in dynamic equilibrium between the gain of helium diffusing from Earth's crust (as a product of radioactive decay) and losses of helium into space.
https://energy.utah.gov/wp-content/uplo ... Plan-1.pdf

I expect that YE creationists honestly didn't realize how the system works; this is probably an error, not an intentional dishonesty. I've seen similar arguments concerning the amount of salt in the oceans. There's a dynamic equilibrium with that, also.

Of course there is always an alternative speculation to overturn obvious conclusions from scientific data that biased participants do not like.

YE creationists do not like the data showing that helium from radioactive breakdown in the Earth continues to replenish helium even as it continues to offgas into space. However, the facts are what they are, and so the "too much helium story" falls apart on inspection.

Since evolution kept regularly pushing back old age estimated timelines there came a point more than 100 year ago when evolutionists had to come up with a different source for the energy of the sun because gravitational contraction proposed by Lord Kelvin meant the sun was no older than 30 million years. The new theory was nuclear fusion which first emerged in 1920.

Turns out, nuclear fusion is a fact. That's what a hydrogen bomb does. Now we can produce nuclear fusion in controlled experiments; it's a promising source of energy, if we can increase the efficiency of the process a bit. No point in denying the fact.

There was a problem with the math and evidence,

In the case of the helium story, there was a problem with the evidence showing helium continuing to form and offgas from the Earth itself. In the words of Thomas Huxley, "a lovely little theory, killed by an ugly fact."
[/quote]

Marke: Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

[The Barbarian]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

[marke]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

[The Barbarian]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

The point is, these guys lied to you about the supposed helium problem with an old Earth. As you now see, the concentration in the atmosphere is a dynamic equilibrium, with new helium replacing helium that leaves the atmosphere.

[marke]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

The point is, these guys lied to you about the supposed helium problem with an old Earth. As you now see, the concentration in the atmosphere is a dynamic equilibrium, with new helium replacing helium that leaves the atmosphere.

Marke: I do not believe critics of Austin's findings are necessarily right just because they said so.

[The Barbarian]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

The point is, these guys lied to you about the supposed helium problem with an old Earth. As you now see, the concentration in the atmosphere is a dynamic equilibrium, with new helium replacing helium that leaves the atmosphere.

Marke: I do not believe critics of Austin's findings are necessarily right just because they said so.

As you see, Austin was confronted about his lie, and admitted it when shown the evidence. The technical reasons he messed up the analysis by including unmelted material and by submitting material he knew was too young to be accurately measured by the method he chose, are things he should have known without being reminded. It all adds up to intentionally trying to deceive.

[marke]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

The point is, these guys lied to you about the supposed helium problem with an old Earth. As you now see, the concentration in the atmosphere is a dynamic equilibrium, with new helium replacing helium that leaves the atmosphere.

Marke: I do not believe critics of Austin's findings are necessarily right just because they said so.

As you see, Austin was confronted about his lie, and admitted it when shown the evidence. The technical reasons he messed up the analysis by including unmelted material and by submitting material he knew was too young to be accurately measured by the method he chose, are things he should have known without being reminded. It all adds up to intentionally trying to deceive.

Marke: Old earth dating methods are built upon too many assumptions and unknowns to be accepted as reasonably accurate.

AI Overview
Learn more
Yes, "old earth" dating methods, particularly radiometric dating, rely on several key assumptions, such as a constant decay rate of radioactive elements and the initial conditions of a rock sample remaining unchanged, which cannot be directly verified and are therefore considered a potential point of criticism by some scientists and creationists; meaning the age estimations depend on these assumptions being accurate.
Key points about assumptions in old earth dating methods:

[The Barbarian]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

The point is, these guys lied to you about the supposed helium problem with an old Earth. As you now see, the concentration in the atmosphere is a dynamic equilibrium, with new helium replacing helium that leaves the atmosphere.

Marke: I do not believe critics of Austin's findings are necessarily right just because they said so.

As you see, Austin was confronted about his lie, and admitted it when shown the evidence. The technical reasons he messed up the analysis by including unmelted material and by submitting material he knew was too young to be accurately measured by the method he chose, are things he should have known without being reminded. It all adds up to intentionally trying to deceive.

Marke: Old earth dating methods are built upon too many assumptions and unknowns to be accepted as reasonably accurate.

AI Overview
Learn more
Yes, "old earth" dating methods, particularly radiometric dating, rely on several key assumptions, such as a constant decay rate of radioactive elements and the initial conditions of a rock sample remaining unchanged, which cannot be directly verified and are therefore considered a potential point of criticism by some scientists and creationists; meaning the age estimations depend on these assumptions being accurate.
Key points about assumptions in old earth dating methods:

Your AI neglected isochrons, by which we can determine the initial state of the rock. Constant rate of nuclear decay is well-documented. The exceptions?

Due to the smaller size of the nucleus compared to the atom and the enormity of electromagnetic forces, it is impossible to predict radioactive decay. The atomic nucleus which is in the center of the atom is buffered by surrounding electrons and external conditions. Because of this, the study of decay is independent of the element's environment. In other words, the decay rate is independent of an element's physical state such as surrounding temperature and pressure. For a given element, the decay or disintegration rate is proportional to the number of atoms and the activity measured in terms of atoms per unit time. If "A" represents the disintegration rate and "N" is number of radioactive atoms, then the direct relationship between them can be shown as below:

A∝N(1)

or mathematically speaking

A=λN(2)

where

A is the Total activity and is the number of decays per unit time of a radioactive sample.
N is the total number of particles in the sample.
λ is the constant of proportionality or decay constant.

Decay Rate & Chemical Kinetics

Since the decay rate is dependent upon the number of radioactive atoms, in terms of chemical kinetics, one can say that radioactive decay is a first order reaction process. Even though radioactive decay is a first order reaction, where the rate of the reaction depends upon the concentration of one reactant (r = k [A] = k [A}) , it is not affected by factors that alter a typical chemical reactions. In other words, the reaction rate does not depend upon the temperature, pressure, and other physical determinants. However, like a typical rate law equation, radioactive decay rate can be integrated to link the concentration of a reactant with time. Also, radioactive decay is an exponential decay function which means the larger the quantity of atoms, the more rapidly the element will decay. Mathematically speaking, the relationship between quantity and time for radioactive decay can be expressed in following way:

dNdt=−λN(3)

or more specifically

dN(t)dt=−λN(4)

or via rearranging the separable differential equation

dN(t)N(t)=−λdt(5)

by Integrating the equation

lnN(t)=−λt+C(6)

with

C is the constant of integration
N(t) is the amplitude of N after lapse of time t
λ is the decay rate constant.

One could derive equation 4 in following manner, too. The decay rate constant, λ, is in the units time-1. For further information about first-order reactions, refer to First-Order Reactions.
https://chem.libretexts.org/Bookshelves ... ecay_Rates

[marke]

Nuclear fusion is a fact but what a shame the speculators had to invent the neutrino that took them 70 years to finally but questionably prove existed.

That's the thing about scientific theories. If they have problems, then scientists try to figure out why. There was no evidence for neutrinos, except that nuclear fusion would require that they exist. So scientists accepted that there were neutrinos, based on the facts at hand.

Later on, scientists were vindicated when the predicted neutrinos were identified. Theories are considered true, when they make predictions that are later confirmed. This probably seems odd to creationists, but nothing humans can do works better for understanding the natural universe.

Marke: Both Christian and non-Christian scientists are researching the various fields of science for answers.

The point is, these guys lied to you about the supposed helium problem with an old Earth. As you now see, the concentration in the atmosphere is a dynamic equilibrium, with new helium replacing helium that leaves the atmosphere.

Marke: I do not believe critics of Austin's findings are necessarily right just because they said so.

As you see, Austin was confronted about his lie, and admitted it when shown the evidence. The technical reasons he messed up the analysis by including unmelted material and by submitting material he knew was too young to be accurately measured by the method he chose, are things he should have known without being reminded. It all adds up to intentionally trying to deceive.

Marke: Old earth dating methods are built upon too many assumptions and unknowns to be accepted as reasonably accurate.

AI Overview
Learn more
Yes, "old earth" dating methods, particularly radiometric dating, rely on several key assumptions, such as a constant decay rate of radioactive elements and the initial conditions of a rock sample remaining unchanged, which cannot be directly verified and are therefore considered a potential point of criticism by some scientists and creationists; meaning the age estimations depend on these assumptions being accurate.
Key points about assumptions in old earth dating methods:

Your AI neglected isochrons, by which we can determine the initial state of the rock. Constant rate of nuclear decay is well-documented. The exceptions?

Due to the smaller size of the nucleus compared to the atom and the enormity of electromagnetic forces, it is impossible to predict radioactive decay. The atomic nucleus which is in the center of the atom is buffered by surrounding electrons and external conditions. Because of this, the study of decay is independent of the element's environment. In other words, the decay rate is independent of an element's physical state such as surrounding temperature and pressure. For a given element, the decay or disintegration rate is proportional to the number of atoms and the activity measured in terms of atoms per unit time. If "A" represents the disintegration rate and "N" is number of radioactive atoms, then the direct relationship between them can be shown as below:

A∝N(1)

or mathematically speaking

A=λN(2)

where

A is the Total activity and is the number of decays per unit time of a radioactive sample.
N is the total number of particles in the sample.
λ is the constant of proportionality or decay constant.

Decay Rate & Chemical Kinetics

Since the decay rate is dependent upon the number of radioactive atoms, in terms of chemical kinetics, one can say that radioactive decay is a first order reaction process. Even though radioactive decay is a first order reaction, where the rate of the reaction depends upon the concentration of one reactant (r = k [A] = k [A}) , it is not affected by factors that alter a typical chemical reactions. In other words, the reaction rate does not depend upon the temperature, pressure, and other physical determinants. However, like a typical rate law equation, radioactive decay rate can be integrated to link the concentration of a reactant with time. Also, radioactive decay is an exponential decay function which means the larger the quantity of atoms, the more rapidly the element will decay. Mathematically speaking, the relationship between quantity and time for radioactive decay can be expressed in following way:

dNdt=−λN(3)

or more specifically

dN(t)dt=−λN(4)

or via rearranging the separable differential equation

dN(t)N(t)=−λdt(5)

by Integrating the equation

lnN(t)=−λt+C(6)

with

C is the constant of integration
N(t) is the amplitude of N after lapse of time t
λ is the decay rate constant.

One could derive equation 4 in following manner, too. The decay rate constant, λ, is in the units time-1. For further information about first-order reactions, refer to First-Order Reactions.
https://chem.libretexts.org/Bookshelves ... ecay_Rates

Marke: Since radiometric test results rely on unverifiable assumptions about decay rates, among other variables, radiometric test results will always be tentative or debatable.

AI Overview
Learn more
Assumptions about decay rates can significantly impact dating results because radiometric dating methods, which are used to determine the age of materials, rely on the premise that radioactive decay occurs at a constant, known rate; if this assumption is incorrect, the calculated age will be inaccurate, potentially leading to over- or underestimation of the true age of a sample.