Are there any practical uses for Darwin's tree in applied biology

[Arete]

4 minutes ago, Sensei said:

It's impossible. I have never heard of virologist or microbiologist disagreeing with microevolution and macroevolution, when they simply see it in their labs on daily basis. That's why they have so much of work (finding new medicament for viruses and microbes), just because of little mutations in microbes every day..

The microbes will take any concept one has of the division between micro and macro evolution, laugh at you and do whatever the hell they want. Different species? Ha, it's a couple of genes that produce a totally different phenotype, and they're on plasmids, and can make the bacteria kill you or be totally harmless. I'm looking at you Bacillus ACT group. 

[Reg Prescott]

29 minutes ago, Arete said:

He was a proponent of Neo-Lamarkian evolution. It wasn't that he has been shunned or ignored, simply that Lamarkism was disproven. 

I know nothing about this dude (yet - gonna write to Santa), but I could easily point you to various places in these forums where our senior members tell us scientific theories are never (or almost never) disproven. And I'd say they're largely right.

Do you believe they can be disproven?

[Arete]

Just now, Reg Prescott said:

I know nothing about this dude (yet - gonna write to Santa), but I could easily point you to various places in these forums where our senior members tell us scientific theories are never (or almost never) disproven. And I'd say they're largely right.

Do you believe they can be disproven?

Of course.  

 

If evolution were disproven tomorrow it would be the most exciting day ever to be an evolutionary biologist. But you'd have to come up with something pretty amazing to better explain the reams of data produced every day which boringly conforms to the predictions of contemporary evolutionary theory. 

[Reg Prescott]

21 minutes ago, Sensei said:

It's impossible. I have never heard of virologist or microbiologist disagreeing with microevolution and macroevolution, when they simply see it in their labs on daily basis. That's why they have so much of work (finding new medicament for viruses and microbes), just because of little mutations in microbes every day..

 

That's generally not the beef. It's not, by and large, that macro and micro evolution are denied; rather the claim is that the processes which account for the latter are unable to account for the former.

[CharonY]

2 minutes ago, Reg Prescott said:

I know nothing about this dude (yet - gonna write to Santa), but I could easily point you to various places in these forums where our senior members tell us scientific theories are never (or almost never) disproven. And I'd say they're largely right.

Do you believe they can be disproven?

Lamarckian was never a fully fledged theory. It was one of the hypotheses that tried to explain how inheritance might work. Once germlines were discovered it was not a workable hypothesis anymore.

2 minutes ago, Reg Prescott said:

That's generally not the beef. It's not, by and large, that macro and micro evolution are denied; rather the claim is that the processes which account for the latter are unable to account for the former.

There is no mechanical distinction between those two. It is just the degree of divergence. The foundation is still genetic in nature.

[Reg Prescott]

I hope Francis won't mind if I slip in a quick link here which might be of interest to our members. Philosopher of biology, Elliott Sober, in his "The Nature of Selection" examines the controversy raised by the model of punctuated equilibrium, and whether or not it poses a threat to the more traditional gradualistic understanding of evolution. Does the idea of species selection undermine the view that conventional micro-evolutionary processes can also be invoked to explain macro-evolution? Gould, Eldredge et al argue for (it does undermine this view); a whole load of other dudes argue against. See pages 356 - 368 (if the link works).

https://books.google.com.tw/books?id=3KGSBgAAQBAJ&pg=PA359&lpg=PA359&dq=Rather,+we+have+here+an+ontological+claim+to+the+effect+that+an+item+at+the+macro-level&source=bl&ots=dws7k550_1&sig=Bt3eN9gbT86zXsZoiTrGSSkQfyk&hl=en&sa=X&ved=2ahUKEwj785fYp7XeAhULXrwKHd0QC0sQ6AEwAHoECAAQAQ#v=onepage&q=Rather%2C we have here an ontological claim to the effect that an item at the macro-level&f=false

You'll find a similar exchange of views in a collection entitled "Contemporary Debates in the Philosophy of Biology".

Now, let no man or woman ever mention it again. 

[Strange]

16 hours ago, Francis said:

I suspect that all the examples you have mentioned here are either based on microevolution (making Darwin's tree irrelevant) or they are theories ("coalescent theory ... predictions of common descent ... assumption ... models ... supports common ancestry") that actually have no practical use in applied science.

!

Moderator Note

This sounds as if you have not read the linked articles. Soapboxing is a violation of rule 2.8. If you are not prepared to engage properly, this thread will be closed.

 

[Reg Prescott]

Francis said in an earlier post:

"You made the claim, so now the onus is on you to back it up - instead of throwing vague examples at me, take just of these examples and explain in specific terms how it demonstrates that Darwin's tree has proven practically useful in applied science.  I'd bet my bottom dollar that you can't."

 

It is manifestly unfair that other members can simply hurl reams of sources, citations and linked articles, expect their opponent to not only read them all, but then spend his entire day constructing a defense, while they sit back and do nothing.

I'd expect our members here to be able to mount their own defenses and argue their own positions, perhaps with the help of sources. Fairness surely demands that they be willing to put in as much work as their opponent.

"Snowing" is certainly an easy way to win a debate, if you call that winning. Simply silencing an unpopular opinion is even easier. And I have a sneaking suspicion that's exactly what's going to happen sometime soon.

[DrP]

10 minutes ago, Reg Prescott said:

It is manifestly unfair that other members can simply hurl reams of sources, citations and linked articles, expect their opponent to not only read them all, but then spend his entire day constructing a defense,

*facepalm*

Yea - it's so unfair that science is backed up by references and tried and tested experiment. lol.

[swansont]

5 hours ago, Francis said:

The cult does not tolerate dissenters.

!

Moderator Note

Your observation that conjecture about your motivations (biblical creationist) are off-topic is correct. Those posts have been removed.

But by the same token, characterizing any of science as a cult also has no place in the conversation. Get back on topic.

 

4 hours ago, Reg Prescott said:

 

With all due respect to your professional expertise, sir, this comment is both philosophically naive and historically unprecedented.

There are no cases at all, that I'm aware of, where all involved in a major theoretical paradigm gasp in horror at some new discovery or observation, concede falsification, and en masse abandon the paradigm, leaving themselves with no theoretical framework.

Do you know of any?

!

Moderator Note

This, and some of your other posts are off-topic. The thread is contentious enough without any attempted hijacking

 

[mistermack]

7 hours ago, Francis said:

Whether I consider Darwin's tree to be "right or wrong" is irrelevant to the OP.

Keep your secrets then. But don't expect to be taken seriously. It turns your effort to debate into a joke. 

[swansont]

21 minutes ago, Reg Prescott said:

Francis said in an earlier post:

"You made the claim, so now the onus is on you to back it up - instead of throwing vague examples at me, take just of these examples and explain in specific terms how it demonstrates that Darwin's tree has proven practically useful in applied science.  I'd bet my bottom dollar that you can't."

 

It is manifestly unfair that other members can simply hurl reams of sources, citations and linked articles, expect their opponent to not only read them all, but then spend his entire day constructing a defense, while they sit back and do nothing.

I'd expect our members here to be able to mount their own defenses and argue their own positions, perhaps with the help of sources. Fairness surely demands that they be willing to put in as much work as their opponent.

"Snowing" is certainly an easy way to win a debate, if you call that winning. Simply silencing an unpopular opinion is even easier. And I have a sneaking suspicion that's exactly what's going to happen sometime soon.

!

Moderator Note

It is also unfair to show up and make claims while being unfamiliar with the topic. The OP was answered, and the response brushed aside with "I suspect that all the examples you have mentioned here..." which is pretty weak tea.

It's also unfair to make such a dismissal but expect others to go into depth with some justification — which wasn't part of the question — especially after the first answer was brushed aside. The OP was free to ask about a specific one and inquire about the details, but tried to shift the burden of the argument.

One last thing, Reg: stop hijacking the thread to kvetch about process. If you can't add to the topic of discussion, don't post in the thread. 

 

  

[Arete]

5 hours ago, Reg Prescott said:

It is manifestly unfair that other members can simply hurl reams of sources, citations and linked articles, expect their opponent to not only read them all, but then spend his entire day constructing a defense, while they sit back and do nothing.

If the OP had a genuine question about the practical utility of phylogenetic inference, I would have thought a handful of review papers explicitly explaining how it is used in various applied fields would be a useful answer - but as was demonstrated it was a disingenuous OP and they were rejected out of hand.

Probably should've just said "Sure bud" and gone back to doing useful things with phylogenies, but hey, I had beer that needed drinking and the TV was boring. 

[StringJunky]

5 hours ago, Reg Prescott said:

Francis said in an earlier post:

"You made the claim, so now the onus is on you to back it up - instead of throwing vague examples at me, take just of these examples and explain in specific terms how it demonstrates that Darwin's tree has proven practically useful in applied science.  I'd bet my bottom dollar that you can't."

 

It is manifestly unfair that other members can simply hurl reams of sources, citations and linked articles, expect their opponent to not only read them all, but then spend his entire day constructing a defense, while they sit back and do nothing.

I'd expect our members here to be able to mount their own defenses and argue their own positions, perhaps with the help of sources. Fairness surely demands that they be willing to put in as much work as their opponent.

"Snowing" is certainly an easy way to win a debate, if you call that winning. Simply silencing an unpopular opinion is even easier. And I have a sneaking suspicion that's exactly what's going to happen sometime soon.

If one attacks the scientific consensus, the onus is on the attacker to support their position, not the other way round. This is the standard expectation in science and discourse here..

Edited November 2, 2018 by StringJunky

[Francis]

On ‎2‎/‎11‎/‎2018 at 3:19 PM, StringJunky said:

Have a chew on this: http://www.talkorigins.org/indexcc/CA/CA215.html

Okay, I finally got around to reading this article, which is quite extensive.  Since you are the one making the claim that this article contains at least one practical use of Darwin's tree in applied science, the onus is one you to point out such an example and then explain how and why.  When you do find one, please let me know, as I will be happy to look in to it.

As you examine each item on the list, ask yourself, "Is this dependant on the information that all life on earth evolved from a common ancestor (a microbe) that existed millions of years ago (ie, Darwin's tree)".  

A word of warning:  Don't be fooled by potentially misleading terms like "proved its usefulness" and "the tree of life" and "evolutionary theory" and "common descent".
 

23 hours ago, Arete said:

No, I just didn't feel it necessary to duplicate literature which already exists because you're too lazy to click a link, but I'll play: 

Here: https://link.springer.com/article/10.1007/BF00182388

Is an investigation of the genus Neisseria  - which includes the pathogens N. meningitidis and N. gonorrhoeae  as well as a number of non-pathogenic commensal species. Both pathogens have been observed in the clinic to be penicillin resistant. By reconstructing the phylogeny ("Darwin tree" if you insist) we can determine that the resistance genes are mosaic genes resultant of ectopic recombination rather than vertical transfer, and horizontal exchange with commensal species is a probable route for inheritance of resistance in pathogenic species. 

TlDr: by Making a Darwin tree of a genus of bacteria, we can show that they share and recombine genes that encode antibiotic resistance, and come up with better management plans for controlling the spread of drug resistance in those pathogens. 

Here is the fatal flaw in your argument:  You have equated the phylogeny of a genus of bacteria to Darwin's tree, so your use of the term, "Darwin's tree" here is wholly inappropriate and misleading.  

A more appropriate term in this case would be "family tree".  The "tree" here is observable microevolution and is confined to a genus, so it is nothing like Darwin's tree, which includes the entire history of life that evolved from a microbe over millions of years.   "Making a Darwin's tree of a genus of bacteria" is therefore an oxymoron.
 Think of it this way:  A biologist who is a Young Earth Creationist (ie, someone who rejects Darwin's tree) could trace and reconstruct the phylogenic "tree"  of these bacteria just as proficiently as any  "Darwinist" biologist.
 

On ‎2‎/‎11‎/‎2018 at 4:01 PM, Reg Prescott said:

Darwinian-type explanations are as vacuous as Aristotelian "the rock falls to achieve its natural place" type, or "morphine puts you to sleep because it has a dormitive virtue".

How dare you!!

Edited November 3, 2018 by Francis

[beecee]

37 minutes ago, Francis said:

A word of warning:  Don't be fooled by potentially misleading terms like "proved its usefulness" and "the tree of life" and "evolutionary theory" and "common descent".

Similar line of argument and attempted exclusions often made by our poor philosopher....I call it attempted  cop outs.

https://en.wikipedia.org/wiki/Applications_of_evolution

Applications of evolution:

Evolutionary biology, in particular the understanding of how organisms evolve through natural selection, is an area of science with many practical applications.^[1][2]Creationists often claim that the theory of evolution lacks any practical applications; however, this claim has been refuted by scientists.

https://www.google.com.au/search?q=Are+there+any+practical+uses+for+Darwin's+tree+in+applied+biology&oq=Are+there+any+practical+uses+for+Darwin's+tree+in+applied+biology&aqs=chrome..69i57j69i60l3.1765j0j7&sourceid=chrome&ie=UTF-8

Descent with modification is one of its most basic assumptions. Diseases and pests evolve resistance to the drugs and pesticides we use against them. Evolutionarytheory is used in the field of resistance management in both medicine and agriculture (Bull and Wichman 2001).

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

On 10/26/2018 at 12:24 PM, Francis said:

I'm no expert, but seems to me that there exist no practical uses for Darwin's tree of common descent in applied biology (or in any form of applied science, for that matter).  I find this rather curious.

And as you start your inference with the above of not being an expert, Içhose to take the view of a reputable reasonable source.

[Francis]

2 hours ago, beecee said:

Creationists often claim that the theory of evolution lacks any practical applications; however, this claim has been refuted by scientists.

I'm not claiming that the theory of evolution lacks practical applications -  as I stated  in an earlier post.  Indeed, I believe the theory of evolution has innumerable practical applications.  My point is that some posters here seem to think Darwin's tree is part of the theory of evolution - but it isn't -  it is a conclusion reached from ToE.  The theory and the conclusion are two separate things - the conclusion needs the theory, but the theory doesn't need the conclusion.

 

Incidentally, in this context, "Creationists" usually refers to Young Earth Creationists.  I am not of that ilk - I believe life began as microbes millions of years ago and through many stages and different life-forms arrived at the creatures of the present age.

Edited November 3, 2018 by Francis

[DrP]

37 minutes ago, Francis said:

 My point is that some posters here seem to think Darwin's tree is part of the theory of evolution - but it isn't -  it is a conclusion reached from ToE.

How is the conclusion not part of the theory?

[Francis]

22 hours ago, Strange said:

!

Moderator Note

This sounds as if you have not read the linked articles. Soapboxing is a violation of rule 2.8. If you are not prepared to engage properly, this thread will be closed.

 

I did read that article, as a matter of fact.  But I haven't yet got around to reading some other links offered to me.  Anyways, I will take your advice on board and read them all.

28 minutes ago, DrP said:

How is the conclusion not part of the theory?

Because a theory and a conclusion from the theory are two different things.  Is the theory dependant on the conclusion?  No.  

Please show me a definition from any scientific website that includes Darwin's tree in their definiton the theory of evolution.  

 

Besides that, the practical usefulness of the theory of evolution is not the subject of the the OP.

Edited November 3, 2018 by Francis

[Strange]

27 minutes ago, Francis said:

Besides that, the practical usefulness of the theory of evolution is not the subject of the the OP.

Can you explain why it is important (or even interesting) whether the descent of species from a common origin has practical uses or not?

 

[DrP]

2 hours ago, Francis said:

Please show me a definition from any scientific website that includes Darwin's tree in their definiton the theory of evolution.

OK, maybe I don't know enough about it - I was under the impression it was part of the extended theory around the subject and the theory of evolution. It seems like it to me but I could be wrong. It is clearly closely related... and seems to be useful to some people. 

[Strange]

23 hours ago, DrP said:

OK, maybe I don't know enough about it - I was under the impression it was part of the extended theory around the subject and the theory of evolution. It seems like it to me but I could be wrong. It is clearly closely related... and seems to be useful to some people. 

There might be some confusion here because there are two parts to the Walace-Darwin theory of evolution: evolution by natural selection and common descent of species. The former doesn't imply the latter but is the mechanism by which the latter is achieved.

The "tree of life" is a consequence of these theories and can be deduced from the fossil evidence, from living species and from DNA. It obviously has practical purposes (as a teaching tool if nothing else) so I'm not sure what the OP's point is. I think we can draw our own conclusions from his caginess on this ...

[Francis]

19 hours ago, Strange said:

Can you explain why it is important (or even interesting) whether the descent of species from a common origin has practical uses or not?

 

It's not important, but it is interesting that so many scientists think Darwin's tree is essential to biology, when it appears that applied biology - by far the most important form of biology - seems to have no need for it at all.   

17 hours ago, DrP said:

OK, maybe I don't know enough about it - I was under the impression it was part of the extended theory around the subject and the theory of evolution. It seems like it to me but I could be wrong. It is clearly closely related... and seems to be useful to some people. 

No, you weren't wrong, actually - I was wrong!  I got the definition of "evolution" mixed up with the definition of "the theory of evolution".  Sorry

On ‎2‎/‎11‎/‎2018 at 3:51 PM, StringJunky said:

Darwin described descent with modification, which the tree illustrates, and those subjects/discipines exploit that principle.

Descent with modification is a fact that doesn't rely on Darwin's tree.  Descent with modification would still be a fact even if life on earth were only a week old.  Applied science relies on facts, not interpretations of ancient history.

 

On ‎2‎/‎11‎/‎2018 at 5:02 PM, Sensei said:

It's impossible. I have never heard of virologist or microbiologist disagreeing with microevolution and macroevolution, when they simply see it in their labs on daily basis. That's why they have so much of work (finding new medicament for viruses and microbes), just because of little mutations in microbes every day..

They see macroevolution in their labs every day? 
Yes, their work depends on  "little mutations in microbes every day" - but Darwin's tree?
 

On ‎2‎/‎11‎/‎2018 at 5:13 PM, CharonY said:

If you have to go back to the beginning of the 20th century to cite someone clinging to a disproven hypothesis to invalidate a routine methodology used by thousands of researcher, you are doing something wrong (and the something wrong is simply being uninformed on the subject matter).

- Pierre-P Grasse died in 1985.

- Another straw man?  Which  "routine methodology used by thousands of researchers" am I attempting to invalidate? 

 

 

On ‎2‎/‎11‎/‎2018 at 9:56 PM, swansont said:

 

Your observation that conjecture about your motivations (biblical creationist) are off-topic is correct. Those posts have been removed.

But by the same token, characterizing any of science as a cult also has no place in the conversation. Get back on topic.

Fair point.  My apologies.

On ‎2‎/‎11‎/‎2018 at 10:21 PM, mistermack said:

Keep your secrets then. But don't expect to be taken seriously. It turns your effort to debate into a joke. 

In other words, you can't give me an example of a practical use for Darwin's tree in applied biology.

On ‎2‎/‎11‎/‎2018 at 10:47 PM, swansont said:

 

It is also unfair to show up and make claims while being unfamiliar with the topic. The OP was answered, and the response brushed aside with "I suspect that all the examples you have mentioned here..." which is pretty weak tea.

What I meant by "I suspect ..." was "To the best of my knowledge ..."

On ‎3‎/‎11‎/‎2018 at 3:29 AM, Arete said:

If the OP had a genuine question about the practical utility of phylogenetic inference, I would have thought a handful of review papers explicitly explaining how it is used in various applied fields would be a useful answer

But the OP didn't have "a genuine question about the practical utility of phylogenetic inference" - it questions the practical utility of Darwin's tree.  Darwin's tree is a map of the entire history of life - beginning with microbes that existed millions of years.  Does phylogenetic inference depend on knowing this entire history of life?  If so, how and why?

On ‎3‎/‎11‎/‎2018 at 3:31 AM, StringJunky said:

If one attacks the scientific consensus, the onus is on the attacker to support their position, not the other way round. This is the standard expectation in science and discourse here..

Which "scientific consensus" am I attacking, exactly?

22 hours ago, beecee said:

And as you start your inference with the above of not being an expert, chose to take the view of a reputable reasonable source.

Which "reasonable reputable source" demonstrates a practical use in applied science for Darwin's tree?
 

On ‎2‎/‎11‎/‎2018 at 3:19 PM, StringJunky said:

Have a chew on this: http://www.talkorigins.org/indexcc/CA/CA215.html

Hey what about this one?  It claims to use "the tree of life" (taken from the same article).

"Ribotyping is a technique for identifying an organism or at least finding its closest known relative by mapping its ribosomal RNA onto the tree of life. It can be used even when the organisms cannot be cultured or recognized by other methods. Ribotyping and other genotyping methods have been used to find previously unknown infectious agents of human disease (Bull and Wichman 2001; Relman 1999)."

 

Edited November 4, 2018 by Francis

[Francis]

On ‎2‎/‎11‎/‎2018 at 3:51 PM, Arete said:

theory is as good as it gets in science

Really?  What about applied science?  In applied science, they actually DO useful stuff, not just talk about theories.

On ‎2‎/‎11‎/‎2018 at 3:51 PM, Arete said:

Believing in micro but not macro evolution is like believing in hours, but not weeks.

... or like believing that dogs can be bred as big as a Great Dane,  but not believing they can be bred as big as an elephant ... or like believing that humans are running 100 meters faster than they were 50 years ago but not believing that one day humans will run it in one second

On ‎2‎/‎11‎/‎2018 at 3:51 PM, Arete said:

I gave you five.

Yes, but I can't see how ony of them are dependant on Darwin's tree - sorry.  Can you explain how just one of the five is dependant on the D-tree?  Thank you

[mistermack]

1 hour ago, Francis said:

In other words, you can't give me an example of a practical use for Darwin's tree in applied biology.

No. So what? Since Darwin's tree is an explanation of the past 3,000 plus million years of evolution, and applied biology is all about the present, then it's not surprising. I don't work in "applied biology" so that's not likely to happen anyway, and you are asking for a "practical" use.

Darwin's tree is self evident once anyone with half a brain is given the outline of how evolution works. It's all about THEORY and UNDERSTANDING of the past. I can't think of a practical use for the big bang theory in applied physics. It's nowhere near as bleeding obvious as Darwin's tree, but it's still accepted Theory in physics. 

And like I said, it's a pointless observation. These things explain the past in a coherent logical and evidence based manner. We no longer have to invent superstitious stories about big ghostly men in the sky making everything in seven days. 

Increasing understanding IS a practical use, in my book, and to me, all of biology is applied biology, because biology's main application has always been to understand the living world. And there's been nothing in the history of biology to remotely match Darwin's origin of species in explaining and understanding that. 

Of course, Darwin's tree can't explain talking snakes and women made from ribs. Or people living to 1,000 years old, or how eating one apple curses the human race for the next six thousand years. 

It DOES explain why we find simpler fossils in older layers of the Earth though. Explains it all perfectly well. To anyone who actually WANTS to know.