Neighbor-joining is rarely used today (it’s memory efficient but difficult to assess how accurate the tree output is) basically telling the computer “draw lines between the closest pair, add the next closest, repeat until all are joined”; parsimony is “draw a tree connecting all of these taxa which gives the lowest total number of changes”; UPGMA is used for precomputed distances (like shape analyses) and is similar to parsimony; Bayesian is somewhat of a magic black box and starts with a randomly chosen tree that it iteratively improves towards one’s preferred characteristic (usually most parsimonious or most likely); maximum likelihood uses a probability for each type of mutation, and then computes which tree is most likely using that.
In terms of the principles and assumptions underlying phylogenetic analyses, it’s no different from using statistical analyses in ecology (which I have done) or stock market forecasting (which I have not done).
It is not designed to find anything else. There maybe other ways to assess DNA but the thrust is in one basic direction, and, surprise ,surprise, you find it!
The tool needs parameters. It needs to know what to look for. It isn’t a "free " choice. It cannot find anything it is not programed to look for. It is not an open mind.
People see patterns in clouds. They identify them and photograph them, but they are basically meaningless.
No one is looking anymore. The answer is Evolution. Now what is the question?
Richard
NB. There comes a point in a discussion where “Devils Advocate” becomes an obsession. I probably passed that point years ago. My faith demands that ToE, as it stands, is not completely true.
And guess what? … It doesn’t find it if it’s not there!
So this objection has no more coherence than somebody saying we can’t measure the height of a tree because meter sticks were designed to make it seem a different height than it really is.
It’s designed to measure. You might as well claim that radioactivity doesn’t exist because Geiger counters are designed to detect radioactivity.
We don’t find it when random sequences are fed into the tools. This is the control. This shows that DNA from organisms is more tree like than random sequences. This is like comparing a drug to a placebo in a drug trial.
That’s a subjective opinion of what a cloud looks like. Phylogenetic signal is an objective measurement of how tree like the data is. They aren’t comparable.
What you are arguing against is doing science to begin with. We aren’t allowed to use telescopes because they are designed to look at stars. We aren’t allowed to measure radioactivity because Geiger counters are designed to detect radioactivity. We can’t measure mass because balances are designed to detect mass. You are so set on finding a new way to deny evolution that you deny everything in science in the process.
That’s completely false. We find tree like structure in a comparison of DNA sequences and we don’t find tree like structure in a comparison of random DNA sequences. You are arguing we should just ignore an empirical, objective measurement in science. Sorry, but scientists aren’t going to throw away data because you don’t like where it leads.
And it all boils down to whether ToE is unique or not. You don’t think so. I do. And no matter how hard I try you cannot see what I do.
A Telescope is designed to enlarge things in the distance to make them easier to identify. It will do that to a star, or a planet, or a comet or even a space station. It is not looking for anything specific.
Science starts without a clue. It looks, it sees, it hypothesises, it confirms or denies.
Yes, Evolution started that way. But now ToE is entrenched. The task is to confirm. You have the answer, you just need to prove it unequivically,
It is the equivelent of someone deciding that Mass and gravity are not actually related. No one is going to follow that up, are they?
You don’t understand the tools or data that you are criticizing.
I see that you are wrong about how these tools work.
They can take that light and pass it through a prism which allows scientists to look at light at specific wavelengths. What they will often see is black lines in the resulting spectra.
Scientists believe that these black lines, called absorption lines, are caused by specific atoms or molecules absorbing light at those specific wavelengths. We can even duplicate these absorption lines on Earth.
According to you, scientists should just throw all of this out because the method was designed to find absorption lines.
The task is to explain the data. That’s the task of all science. The best tool we have for explaining data in biology is the theory of evolution. Why do we see a measured tree like structure in DNA data? The theory of evolution predicts that we should see a tree like structure in the data, so it explains the data.
We don’t need to prove evolution. We need to understand the data.
You would reject the existence of mass and gravity because the tools we use to measure mass and gravity were made to detect them.
Or the other equivalent, you have decided that organisms are not related to one another, so you won’t follow up on even looking at the evidence.
It is looking for “is this DNA more alike to that DNA or the other DNA?” Repeat. That is all you have to ask and you will inescapably end up with a tree. What other results might you expect?
No, it wouldn’t. A lot of things in geology use the same sort of pathways, analyzing the chemical makeup of rocks. One example is volcanology where geologists can tell which volcano a hundred or miles inland produced a cape on the coast despite the fact that the lava had to flow underneath a valley full of soft sediments and pass between mountains in the growing coast range – all depending on the chemical composition of the igneous rock at the coast differing by less than 0.2% from the lavas of multiple volcanoes. They can even roughly date the eruptions because the mix in a volcanic magma chamber does not stay constant but changes over time.
Those same means are used to find distant relatives (and not just in humans). I recall a case where a will was contested which triggered a secret clause that if it was contested then everyone wishing to inherit would have to undergo DNA testing to establish whether they really were blood relatives of the deceased. Some interesting things were discovered about that particular family tree, though unfortunately for anyone hoping for hot gossip the results were sealed for a few decades except whether or not someone qualified as an heir.
An interesting tidbit:
a reasonable expectation that his trash would be thrown away, not collected
I’ve learned that trash ownership laws vary wildly from place to place. In many locations, the moment unfinished pizza is left on a vacated table it becomes the property of the pizza place, and it may remain their property until it is actually deposited in a garbage truck while in others the moment it goes in a trash bin outside the pizza place it is the property of the garbage service.
That’s a better analogy than most that have been given.
It reminds me of how the Periodic Table of the Elements got filled in: things showed up in spectrographs now and then that couldn’t be accounted for but suggested an unknown element. By Richard’s reasoning, all those should have been thrown out because the tools were designed for finding elements.
@T_aquaticus produced what he claimed was the transitions from Dinosaur to bird. But it was both incomplete and, IM(not so)HO included some dubious connections.
Plus the goalposts keep changing.
One minute the transition is from reptile to Mammal, the next it is from an endothermic dinosaur, thereby cancelling out the major change of metabolism, that is the cause of much of the problems. (except birds are also from that line)
And that is only one of several million transitions within the fauna population of the world.
To be fair, you only have to prove that evolution can actually cross species, let alone “classes” (out of date name)
The basic evidence that started all this was only specialisations within specific animals (Finches & tortoises, I think) The extrapolation that Evolution can create new species or transform a fish into a land creature, has never been confirmed. Even Mud Skippers and lung fish are only curiosities rather than lynch pins.
So get off your high horse
(I have been arguing this for a very log time)
Interesting side note (of which you are probably aware). Helium was based on the Greek root Helios because it was first discovered in the Sun through absorption lines. So we found helium on the Sun before we found it on the Earth.
Then what criteria are you using to determine if a fossil is transitional?
The criteria I am using are the standard ones.
I have shown you fossils that have a mixture of features from modern birds and non-avian dinosaurs. They are transitional by the criteria I am using.
There is more than one lineage in existence. They are all evolving. Why is this considered shifting the goal posts? Is it your belief that only one lineage out of billions on the Earth are allowed to evolve?
Also, species are all that exist in nature. Classifications such as genus, class, order, family, etc. don’t exist in nature. The Linnaean groups are arbitrary. For example, there is nothing stopping us from putting humans and the great apes into a single genus.
It seems that you have already stated that no fossil or DNA evidence would convince you. So what evidence are you looking for?
No, I said that there is no complete record. All you have is some creatures showing traits of others. They are found on all four corers of the globe (Metaphorical corners) with little to indicate that they interacted or progressed further.
Look, I know I am asking for the impossible. It will always boil down to whether the individual accepts or rejects the evidence at any given time. Half full or half empty? The same result but a different perspective.
It is not an argument either of us will ever win, and, even if I won, it would not change the world view.
@St.Roymond 's divinometer is just an excuse for a Christian standpoint.
It is that simple. You are just another blatherskite.
But somehow during that long time you never got round to looking up any details about early human migration to Australia or the Americas, and thought they were somehow supposed to have evolved there independently.
If we had multiple fossils from every species that ever lived we would also see some creatures showing traits of others. I don’t understand your criticism here.
Are you saying that we can’t have transitional fossils until we have multiple fossils from every species that ever lived?
How do you determine this?
If fossils with a mixture of dinosaur and bird features aren’t evidence, then I am confused as to what you would consider evidence.
