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Author Topic:   Who Owns the Standard Definition of Evolution
Taq
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Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 136 of 698 (915055)
02-09-2024 6:25 PM
Reply to: Message 92 by ICANT
02-08-2024 4:06 PM


ICANT writes:
2. Characteristics:
...... Testability: Scientific theories are testable and make verifiable predictions.
....... Explanation: They describe the causes of a particular natural phenomenon.
........Application: These theories are used to explain and predict aspects of the physical universe or specific areas of inquiry, such as electricity, chemistry, and astronomy2.
That perfectly describes the theory of evolution, as shown here:
29+ Evidences for Macroevolution: The Scientific Case for Common Descent
That's 29+ testable predictions made by the theory and confirmed by repeatable observations.

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 Message 92 by ICANT, posted 02-08-2024 4:06 PM ICANT has not replied

  
Taq
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Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


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Message 139 of 698 (915058)
02-09-2024 6:36 PM
Reply to: Message 107 by K.Rose
02-09-2024 12:10 PM


Since I am a working research biologist who deals with theories, hypotheses, and facts on a daily basis perhaps I can shine a light on how scientists view the workings of science and some generalities about evolution. This post will be followed by specific evidence for the theory of evolution.
K.Rose writes:
Scientists and Engineers understand the importance of observation and experimentation/testing, and the proper presentation of conclusions and their Certainty, including the Margin of Error, Probability, and Confidence, all derived using standard statistical methods. Note that Scientific Fact has a pretty high Certainty bar: Zero Error, 100% Probability, 100% Confidence.
First, a bit on theory and hypothesis. A scientific theory is an overarching model. We then construct specific and testable hypotheses based on the theory. For example, the Theory of Atoms proposes that atoms have a nuclei made up of protons and neutrons. Rutherford constructed a specific hypothesis that a beam of protons would result in some protons being deflected as they struck the positively charged nuclei. He ran the test, and sure enough he was able to measure proton deflections. In the same way, the Theory of Evolution can be used to make specific predictions about specific datasets, such as found here:
29+ Evidences for Macroevolution: The Scientific Case for Common Descent
We also need to clarify the differences between hypotheses and observations. These are two different things. We don't observe the hypothesis. We test the hypothesis with observations. Repeatability in science refers to the observations, not the hypothesis.
Facts are observations. Contrary to what you claim, observations come with error bars. In fact, I don't trust a measurement unless I am given error bars. Theories attempt to explain why we see the facts we do. As SJ Gould put it:
quote:
Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.
--SJ Gould, "Evolution as Fact and Theory"
https://wise.fau.edu/...s/knowing/gould_fact-and-theory.html
If Evolutionism can meet the high bar of Scientific Fact, then it should be presented as such. If not, then the Certainty of Evolutionary conclusions must be divulged front and center.
Theories never become facts. They are different things. No idea in science gets higher than theory. Facts are observations. Theories are explanations of the observations.

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 Message 107 by K.Rose, posted 02-09-2024 12:10 PM K.Rose has not replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 144 of 698 (915063)
02-09-2024 6:40 PM
Reply to: Message 133 by sensei
02-09-2024 6:09 PM


sensei writes:
Then you should be able to easily find one example where your evidence proves common ancestry of all animals
The nested hierarchy is proof beyond a reasonable doubt that animals share a common ancestor. This has been understood since the 1800's, and has only been further supported by the much more specific and granular evidence found in genetics.
quote:
Now, since the days of Linnæus this principle has been carefully followed, and it is by its aid that the tree-like system of classification has been established. No one, even long before Darwin's days, ever dreamed of doubting that this system is in reality, what it always has been in name, a natural system. What, then, is the inference we are to draw from it? An evolutionist answers, that it is just such a system as his theory of descent would lead him to expect as a natural system. For this tree-like system is as clear an expression as anything could be of the fact that all species are bound together by the ties of genetic relationship. If all species were separately created, it is almost incrediblepg. 24 that we should everywhere observe this progressive shading off of characters common to larger groups, into more and more specialized characters distinctive only of smaller and smaller groups. At any rate, to say the least, the law of parsimony forbids us to ascribe such effects to a supernatural cause, acting in so whimsical a manner, when the effects are precisely what we should expect to follow from the action of a highly probable natural cause.
--George Romanes, "Scientific Evidences of Organic Evolution"
The Project Gutenberg eBook of The Scientific Evidences of Organic Evolution, by George J. Romanes, M.A., LL.D., F.R.S.

This message is a reply to:
 Message 133 by sensei, posted 02-09-2024 6:09 PM sensei has replied

Replies to this message:
 Message 147 by sensei, posted 02-09-2024 6:51 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


(1)
Message 146 of 698 (915065)
02-09-2024 6:50 PM
Reply to: Message 143 by K.Rose
02-09-2024 6:40 PM


K.Rose writes:
If the random, non-directed evolution of one life form to another has been observed in operation and reproduced in the lab then please share the details.
Evolution is directed by natural selection. It is mutations that are random. Both have been demonstrated in experiments back in the 1940's and 50's.
Plate replica experiment, Lederbergs (1952) :
REPLICA PLATING AND INDIRECT SELECTION OF BACTERIAL MUTANTS - PMC
Fluctuation experiment, Luria and Delbruck (1943):
MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE | Genetics | Oxford Academic
For example, if we take one of the evolution diagrams showing the myriad life forms emanating from a common ancestor, how certain are we of its accuracy?
Very. For example:
quote:
So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 1038 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439).
29+ Evidences for Macroevolution: Part 1
That's a match between independent phylogenies with a 1 in 1x10^38 probability. This is exactly the match the theory of evolution predicts we should see, and that's exactly what we see. Also:
quote:
The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of "the great chain of being" and the continuums predicted by Lamarck's theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.
. . .
The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).
29+ Evidences for Macroevolution: Part 1
How well data fits a tree is quantitatively and statistically measured, and the theory of evolution predicts and explains why we see this quantifiable tree structure in life. ID/creationism can not explain this data.

This message is a reply to:
 Message 143 by K.Rose, posted 02-09-2024 6:40 PM K.Rose has replied

Replies to this message:
 Message 200 by K.Rose, posted 02-10-2024 5:24 AM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 148 of 698 (915067)
02-09-2024 6:51 PM
Reply to: Message 142 by sensei
02-09-2024 6:39 PM


sensei writes:
Cute argument, but very, very weak and far from being close to being any proof. Nowhere is there a rule that says that a pattern is proof of relationship.
That's how science work. The rule is that if your hypothesis predicts a specific pattern in the data and that pattern is observed then the hypothesis is supported. This is how all science works.

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Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 149 of 698 (915068)
02-09-2024 6:53 PM
Reply to: Message 147 by sensei
02-09-2024 6:51 PM


sensei writes:
And how have you determined that? How have you scientifically measured this level of doubt. And how high or how low is it?
Here:
quote:
So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439).
29+ Evidences for Macroevolution: Part 1

This message is a reply to:
 Message 147 by sensei, posted 02-09-2024 6:51 PM sensei has replied

Replies to this message:
 Message 152 by sensei, posted 02-09-2024 6:58 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


(2)
Message 150 of 698 (915069)
02-09-2024 6:56 PM


Mutations Confirm Common Descent
A copy of my post from another thread containing evidence that even sensei was impressed with:
It isn't just the pattern of similarities that evidence common descent and evolution. The differences also provide us with big pieces of evidence.
The inspiration for this post comes from EvoGrad and Stephen Schaffner, from whom I will be borrowing various figures. Ebersberger et al. (2002) published on this subject, and could have served as direct or indirect inspiration for EvoGrad and Schaffner.
With credit given, let's move on to the evidence.
Mutations are heritable changes, specifically heritable changes in the DNA sequence of a genome. The type of mutation I will be discussing is a substitution mutation where one base is swapped out for a different base. For example:
AGGCTAATCG --original
AGGGTAATCG --mutated
There are two main types of substitutions: transitions and transversions. They are called this because if the mutation is between two similar bases it is a transition, and a transversion if it is between two dissimilar bases. The two classes of bases are purines and pyrimidines. For clarity's sake, I like to refer to them as one ring and two ring bases, as shown in the picture below:

credit: EvoGrad
Due to the biochemistry of genetics, transitions tend to happen more often than transversions. That is, substitutions occur more often between bases that have the same number of rings. Even though there are two possible transversion mutations per base compared to just one possible transition, we still see more transitions than transversions.
Evograd compiled a total of 220,000 de novo (i.e. new mutations detected in experiments in green) human mutations from various papers and compared them to 78.6 million substitutions found in the existing human population (i.e. the standing variation in the human population in blue) from public databases. This is what that comparison looks like:

credit: EvoGrad
Like I stated earlier, transitions outnumber transversions in this figure. The first set of bars are the transitions, and the other three sets of bars are the transversions. Also, the rate at which these mutations occur in real time matches the standing variation in the human population. In other words, this is smoking gun evidence that the process we observe creating mutations in real time is responsible for the variation we see in the human population. The fingerprint produced by the natural process of mutation is measurable and present in the human population.
But what if we do the same thing for a comparison of the human and chimp genome? The model for common descent and evolution states that humans and chimps share a common ancestor. Therefore, this model predicts that our lineages started from the same ancestral genome and population. As our lineages diverged, the same process of mutation should have created differences between those lineages. Therefore, if this model is correct then we should see the same fingerprint when we compare the human and chimp genomes.

credit: EvoGrad
Wouldn't you know it, there's that fingerprint. In fact, let's extend it out to other primates:

credit: Schaffner
There's that same fingerprint, just as we would expect from common ancestry and evolutionary mechanisms.
This is smoking gun evidence for common ancestry. This evidence is exactly what we would expect to see if our models are true.
In science we like to use statistics to measure the fit between data and model, so we should do the same for spectrum of mutations. Luckily, Francioli et al. (2015) have already done this for us. They compared mutations in the context of three base pair motifs, as well as in the context of CpG and non-CpG mutations (a subject I will probably touch on later).

Figure 6 | Correlation between observed de novo mutation rates and human/chimp substitution rates for mutation types in different trinucleotide contexts. De novo mutation rate spectrum (Y-axis) is plotted against substitution rate spectrum inferred from human vs chimp comparison (X-axis). Each dot represents a type of mutation in a specific trinucleotide context. The Pearson’s correlation coefficient r2 = 0.993. Figure from Francioli et al. (2015) (Supplemental Figure 6).
An r-squared of 0.993 means that the processes we observe producing mutations in genomes explains 99.3% of the differences observed between the human and chimp genomes. You don't often see this tight of a regression in biology or genetics.

Replies to this message:
 Message 158 by sensei, posted 02-09-2024 7:23 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 153 of 698 (915072)
02-09-2024 7:04 PM
Reply to: Message 152 by sensei
02-09-2024 6:58 PM


sensei writes:
I only see odds of certain observations.
That's exactly what you asked for:
"And how have you determined that? How have you scientifically measured this level of doubt. And how high or how low is it?"--sensei
You clearly don't understand the difference between the odds of an observation and the odds or level of doubt for a theory being true or not.
Those are one in the same. The often used p value in science refers to the chances that a random set of data will produce a false positive. In the case of the match between the independent trees of morphology and the sequence of cytochrome c that probability is 1 in 1x10^38.

This message is a reply to:
 Message 152 by sensei, posted 02-09-2024 6:58 PM sensei has replied

Replies to this message:
 Message 159 by sensei, posted 02-09-2024 7:28 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 155 of 698 (915074)
02-09-2024 7:12 PM
Reply to: Message 120 by ICANT
02-09-2024 4:17 PM


ICANT writes:
The problem with evolution as I see it is that it is built on a lot of assumptions.
I challenge you to name even one that is specific to evolution and not an assumption used for all of science (e.g. scientific laws are consistent through time and space).
The biggest problem evolutionist have is how life began to exist from non life.
Baloney. We don't need to know how life started in order to determine how life changed once it was here. Not one word of the theory of evolution would need to be changed if God created the first replicators that gave rise to all biodiversity through evolutionary mechanisms. Even Darwin stated that the first life could have been created, and he even suggested that there were multiple origins:
quote:
There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
--Charles Darwin, "Origin of Species"
https://www.talkorigins.org/faqs/origin/chapter14.html

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Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 157 of 698 (915076)
02-09-2024 7:17 PM
Reply to: Message 123 by ICANT
02-09-2024 4:31 PM


ICANT writes:
Science? can't find the beginning to exist of one lifeform, and you are wanting to suggest a second lifeform beginning to exist?
Apparently your parents didn't teach you about the birds and the bees. You don't know about biological reproduction?

This message is a reply to:
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Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 160 of 698 (915080)
02-09-2024 7:29 PM
Reply to: Message 158 by sensei
02-09-2024 7:23 PM


Re: Mutations Confirm Common Descent
sensei writes:
Because by similar reasoning, goes like this.
We see that diet changes can happen quite a lot. But most often, it does not change from carnivore to herbivore or the other way around. Far more often, carnivor remains carnivor and herbivor remains herbivor.
Where is your data? What about omnivores? What about extinctions?
Nothing you are presenting is an issue. If food runs out for carnviores then they die out. Carnivores can also move to a different area, or hunt a different species.
With mutations in DNA, it is built in a certain way so it can function. If one change in DNA changes the structure more than another change, than that change is also more likely to cause a decrimental change in function.
That doesn't mean anything. "Built a certain way" means nothing. We need to see data.
So bottom line is, even without your model, with two distinct species without common ancestry, the idea that the species were built in certain ways and the observations that you showed, could easily fit and be compatible as well.
HOW?????
First, if species were separately created why would they even use the same genetic systems? Why would they use the same tRNA's and codons, as one example? Why would we see a nested hierarchy? Why would we see an excess of transitions over transversions when comparing their genomes?
You lack data. You lack specific testable hypotheses. You lack even a meaningful understanding of what the evidence is.

This message is a reply to:
 Message 158 by sensei, posted 02-09-2024 7:23 PM sensei has replied

Replies to this message:
 Message 162 by sensei, posted 02-09-2024 7:36 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 161 of 698 (915081)
02-09-2024 7:35 PM
Reply to: Message 159 by sensei
02-09-2024 7:28 PM


sensei writes:
Common mistake in statistics. Those are certainly not the same.
Yes, they are.
If I have a model where every coin toss is 50-50 random, and I find 10 successive coin tosses to be tails, those odds would be less than 0.1%.

That does not mean that my model has of 50-50 random, has less than 0.1% chance to be true. You need to go back to statistics lessons.
That's now how it works. This is something closer to how the original Student's t-test was worked out.
You claim that you can predict the flip of a coin. After 10 tosses you correctly predict all 10 flips. The chances of you randomly choosing correct is 2^10, or 1 in 1024. Therefore, the p value is 1/1024 or 0.09765625%.

This message is a reply to:
 Message 159 by sensei, posted 02-09-2024 7:28 PM sensei has replied

Replies to this message:
 Message 163 by sensei, posted 02-09-2024 7:38 PM Taq has replied
 Message 165 by sensei, posted 02-09-2024 7:40 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 164 of 698 (915084)
02-09-2024 7:40 PM
Reply to: Message 162 by sensei
02-09-2024 7:36 PM


Re: Mutations Confirm Common Descent
sensei writes:
Why do cars from different brands, have same systems?
They often don't. Cars can use diesel or electric motors. They can use automatic, manual, or CVT's as their transmissions. They can use completely different software written with different machine languages.
More to the point, cars don't fall into a nested hierarchy.
You also failed to even address what I wrote. Why would separately created species need to use the same tRNA's and codons? There is no physical law that requires the relationships seen between the anti-codons on tRNA's and the amino acids attached to them. The relationship is arbitrary. So why do we see the same genetic systems when they don't have to be the same in order for life to function?

This message is a reply to:
 Message 162 by sensei, posted 02-09-2024 7:36 PM sensei has replied

Replies to this message:
 Message 168 by sensei, posted 02-09-2024 7:43 PM Taq has replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


(1)
Message 166 of 698 (915086)
02-09-2024 7:42 PM
Reply to: Message 163 by sensei
02-09-2024 7:38 PM


sensei writes:
Lol, no they are not. If you are so clueless on this matter (especially even after I showed a clear example), you should not do science, honestly.
Your example showed no such thing. I am a scientist, and I use statistics all of the time. What research do you do? What science do you do? What statistical tests do you use? Also, a bit of history:
Lady tasting tea - Wikipedia

This message is a reply to:
 Message 163 by sensei, posted 02-09-2024 7:38 PM sensei has not replied

  
Taq
Member
Posts: 10158
Joined: 03-06-2009
Member Rating: 4.4


Message 167 of 698 (915087)
02-09-2024 7:43 PM
Reply to: Message 165 by sensei
02-09-2024 7:40 PM


sensei writes:
How likely is it that the coin was indeed very close to 50% chance for heads and 50% chance for tails each toss?
We are testing the method for predicting whether the next toss will be heads or tails. Please read what I wrote.

This message is a reply to:
 Message 165 by sensei, posted 02-09-2024 7:40 PM sensei has replied

Replies to this message:
 Message 170 by sensei, posted 02-09-2024 7:48 PM Taq has replied

  
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