Scientific Evidence for Universal Common Descent

[Polymath257]

All that does is show BOTH dog breeds and wolves as tips of the canid tree.

Genetically, the wolf is the same as a dog. They can interbreed, which shows them as the same 'species', and they are similar both morphologically and genetically. There is more diversity among canids than most other haplogroups, yet they have not become reproductively isolated.

The condition of domestication is a man bred trait.. genetically, the wolf and dog are of the same haplogroup, or genotype. IOW, the wolf (many varieties) are just canids, like dogs. They descended from the same ancestor, and became morphologically homogeneous through man made or natural selection.

There is still a lot of variability within canidae, and new breeds (of all canids) continually present themselves. But the SOURCE of that genetic information is deep within the gene pool, and has limited presentation. There is no mechanism to 'create' new traits. Only by 'selecting' the traits, can they become regular occurrences in the new clade or breed.

Again, I described one common mechanism for producing new traits: duplication of genes along with subsequent mutation.

Now, in such a situation, the duplicate would exist in the parents, but the mutation would only show up in the children.

Would an example of such a situation, where we can pinpoint when the mutation occurred and show it did not exist in that gene line prior to that event, would that be enough for you to accept that new traits can be produced?

Alternatively, what sort of evidence would be acceptable for showing that modern traits in dogs did not exist in the ancestral population? Would we need to do a genetic analysis from ancient wolves and how many such would be required for you to be convinced a trait didn't exist in the ancestral population?

Why is it not enough to show that the dog traits don't exist anywhere in the modern wolf population? Or where we can point to when the trait was first expressed? Would you need a genetic analysis of the parents of the dog where the trait was first expressed?

 

[Subduction Zone]

1. What 'evidence!'? That is the point of this thread, to examine this alleged evidence.

Once again I must remind you that you like dad do not even know what is and what is not evidence. Why are you afraid to discuss this topic?

2. You BELIEVE in 'Really Smart People', who you think have 'all this evidence!' But it is indoctrination, not science. There is no evidence, as is painfully evident to the indoctrinees here, so they lash out at me, personally.

That is extreme ignorance at best and appears to be a lie since you have been only given evidence. I find that I have to remind you again that you do not understand the concept of scientific evidence. And you are now guilty of what you would call "ad hom".

3. The scientific method is not owned by ideologues nor propagandists. Anyone with minimal reasoning ability can employ it as a dispassionate tool of discovery.

I am glad that you do not think that the scientific method is owned by creationists. And yes, anyone can use the scientific method. In fact the only thing stopping creationists from using the scientific method is their own fears. I have yet to see a creationist that is not a coward when it comes to applying the scientific method to their beliefs.

4. The BELIEF in common descent is a fine religio/philosophical, belief/opinion. It just lacks scientific credibility and evidence, and is NO WAY, 'settled science!', like the indoctrinees believe.

No, no no. Now this is a lie. By now you have no excuse for making this claim. That you run away when a reasonable offer is given to discuss the nature of evidence tells us that you know that what you claim is false.

5. There IS an anti-Christian, anti-God agenda, with ideologues promoting THEIR religious opinions/worldview, and banning any from the competition. Whether this is 'evil!' .... ..i leave to you.

No, sorry. The theory of evolution is not anti-Christian. It is not anti-God. It goes against your flawed version of God, but there are countless Christians that do accept these facts. Just because your faith is weak is no excuse to attack the science that you do not like.

One more time I offer to discuss the nature of evidence and the scientific method. We do not need to discuss evolution while we do so. All you need to do is to learn what is and what is not evidence.

 

[Subduction Zone]

Flaws in the theory of common descent:

Breeding/Natural Selection

If common descent was a real phenomenon, new genes, new traits, and new genotypes would be appearing all the time. But what do we observe? The opposite.

1. Breeding and natural selection are a DEVOLVING process. Fewer traits become available, as specific ones are 'selected' by man or nature. Eventually, a very narrow, homogeneous morphology is all that remains.

This is incorrect and you of course used a bogus phrase. Natural selection is only one of the main driving forces of evolution. You need to take into account the fact that variation, which adds "information" and natural selection are both constantly functioning. Variation adds "information" both good and bad. Natural selection removes harmful variations.

2. It is BELIEVED and ASSERTED, that new traits and genes are 'created', on the fly, by living organisms, but other than the adaptability of some bacteria and viruses, there is nothing to observe, and no mechanism to define that process in all other living things. We can't even identify it in bacteria and viruses, just assume it, based on their ability to adapt.

No, please do not accuse others of your sins. It has been observed and tested. And there are several known mechanisms. Why not ask questions instead of making blatantly false claims?

3. Organisms that devolve into low diversity conditions, do not conjure up new adaptive traits. They go extinct, locked in the limited selection of their gene pool.

That is because organisms do not "devolve". Once again you ignore variation.

4. The phylogenetic tree, for each distinct haplogroup/genotype/family/genus.. is a record of decreasing diversity, as the tips of the branches show LESS DIVERSITY, than the parent organisms. They become locked in genetic homogeneity, and if their environment changes, and they lack the necessary traits to adapt, they go extinct.

This is a claim that you need to support. Please find articles from well respected professional scientific journals that make this claim. It only looks as if you are lying when you post this nonsense

5. Those who claim that living things 'create' new traits, genes, and features are tasked with defining and demonstrating the mechanisms involved. Merely asserting it, or believing strongly, or ridiculing alternate caricatures, does not provide evidence for this belief.

That has been done time after time. You simply reject the science because it goes against your mythology.

This alleged phenomenon cannot be observed, is contrary to observable, experiential science, and becomes more absurd as the science of genetics unfolds. It is a belief, dogmatically indoctrinated into gullible people from infancy. Someday, it will go the way of flat earth theories, spontaneous generation, leeches, and the 4 humors, but it is the Officially Mandated Belief, for now.

Of course it can be observed. Why do you think that it cannot be? Once again find a paper from a well respected professional scientific journal that supports this claim.

It is such a pity that the concept of scientific evidence scares the pants off of you. You could learn if you could understand this simple concept.

 

[Subduction Zone]

Why is it not enough to show that the dog traits don't exist anywhere in the modern wolf population? Or where we can point to when the trait was first expressed? Would you need a genetic analysis of the parents of the dog where the trait was first expressed?

This is a very apt question. Creationists love to use odds arguments but I myself would love to see the odds of certain traits only being inherited by dogs and somehow lost by the wild wolf population. Not just one trait, but trait after trait.

 

[metis]

This is a very apt question. Creationists love to use odds arguments but I myself would love to see the odds of certain traits only being inherited by dogs and somehow lost by the wild wolf population. Not just one trait, but trait after trait.

And the odds argument doesn't logically work anyway because if something actually happens, the odds if it happening is 1:1.

 

[Subduction Zone]

And the odds argument doesn't logically work anyway because if something actually happens, the odds if it happening is 1:1.

Yes, one has to be very careful when setting up the question. I suppose a creationist can claim that all of the wolves with "doggy genes" could have been forced by God to breed separate from other wolves. But that seems to be a very strange thing for God to do. It is rather obvious that if the genes already existed in the genome, as our creationist seems to believe, that it is very difficult to explain how those genes ended up only in dogs.

 

[Bear Wild]

So much fallacy..
1. Post ONE. I'll look at it. I examined your journalistic fluff piece in detail, yet you still attack me with righteous indignation and outrage..
2. My BELIEFS about the existential nature of the universe are irrelevant. This is about scientific evidence for common descent.
3. My agenda is to have a scientific debate. Unfortunately, i have mostly hecklers and ideologues, outraged that anyone dares to question the sacred tenets of their faith..

YOUR agenda, it seems, is the pathetic, 'Atheists vs Christians!' .... flame war..

'Blasphemer!'.. 'Kill the infidel!!' ...

E.coli? Fluff pieces from journalists cheering computer models?
No, i dutifully examine even the most inane bits of 'evidence' presented, and only 'Ignore!!' (Lying Fool!! .... Blasphemer!!).. the ones dripping with ad hom and ridicule. i will not give them the credibility of response. That is the tactic.. flood the thread with hysterical deflections, poisoning the well, and more ad hominem than you can even note. ..anything but science..

I have only my scientific mind, training, and experience, to shrug off the barrages of UNSCIENTIFIC personal attacks.

I look at the evidence. Present it, if you can, if it is so plentiful and compelling.

I believe you guys are (rightfully) afraid of me. I dispassionately examine everything you produce, and expose it as wishful thinking and belief. You have NOTHING, as valid scientific evidence for your religious belief in common descent.

If you had ANY evidence, you'd present it in a civil, scientific manner, not under pretense.. shrouded in the ravings of jihadist ideologues..

My offer stands:

1. Provide ONE bit of evidence, supported by a link, if desired, or referencing a study.
2. Make your point, clearly showing HOW it supports the theory of common descent.
3. I will review the evidence, and provide additional perspective, if warranted.
4. You can then refute or reply to my rebuttal, and a civil examination of a scientific theory can take place.

But page after page of indignant hecklers and jihadist ideologues, afraid to debate the science, and hell bent on disruption, is not a scientific discussion.. it's not even a philosophical discussion. I can only point out the irrational, unscientific practices of the propagandists and ideologues.

Here you go again heckling those that provide real evidence which you cannot do.
The first study was evidence ( actual real evidence which you have not provided yourself) about E. coli genetic changes. It shows a piece of the complex evidence for common decent and you dismissed it yet is real evidence not your comical comments.

www.ohio.edu/plantbio/staff/showalte/PBIO%20427%20&%20527/Genome%20evolution%20and%20adaptation.pdf

The second was real evidence also about the FOXp2 gene which there is considerable evidence showing the genetic changes in even a single locus has profound influence one the presentation in the organism.

FOXP2 variation in great ape populations offers insight into the evolution of communication skills.
site for the full study is below
www.nature.com/articles/s41598-017-16844-x

With your "scientific mind, training and experience" you should show evidence why the findings of the studies are incorrect first. Evidence not opinion. If you accept the evidence as correct then further studies can be provided. Remember you have a scientific mind and training so give the evidence to refute what has been present. You opinion means nothing. Your silly words and insults mean nothing.

I also asked for your evidence against the fossil record. You have provided nothing. No a single supportive study to explain why the fossil record is incorrect

You have spent 40 years giving your opinion now back it up with your evidence unless you are afraid to and hide behind meaningless opinions.

So Mr. Scientist give us your best evidence against what is provided and you evidence of support for your opinion.

 

[Bear Wild]

BTW, Poly, thanks for the civil, rational discussion. I was beginning to despair that to be possible in this environment!

But the fact is you are not civil or rational!!!! You despair because you have only opinion and no evidence.

 

[Darkstorn]

BTW, Poly, thanks for the civil, rational discussion. I was beginning to despair that to be possible in this environment!

Sucking up to the mods i see. I thought most of your opponents were equally civil compared to Polymath. So this seems like a "stealth" attack against everyone else, while being very careful not to anger staff...

His posts literally contained LESS actual evidence and more of his own explanation than most of your opponents.

I mean, your dishonesty isn't in question, so it'd be pointless for me to try and hammer this fact any further, but it'd be nice if you didn't pretend he was being any better than anyone else. Because that really skews the real narrative of this thread:

You constantly crying "ad hominem" when someone disagrees with you in any capacity(except for Polymath, of course.) Yet in the very same posts you keep making those statements, you actually use extremely hostile language.

I don't care if this gets moderated, but here's my opinion of you: You're a dishonest, hypocritical rhetorician with zero content in your output. Only quantity. And anyone with even an ounce of decency should consider you nothing better than a pathetic piece of discarded rags.

 

[tas8831]

4. The phylogenetic tree, for each distinct haplogroup/genotype/family/genus.. is a record of decreasing diversity, as the tips of the branches show LESS DIVERSITY, than the parent organisms.

So where is the mastiff/pug/chihuahua/boxer/poodle?

They become locked in genetic homogeneity, and if their environment changes, and they lack the necessary traits to adapt, they go extinct.

Or Yahweh slaughters them in a flood.

5. Those who claim that living things 'create' new traits, genes, and features are tasked with defining and demonstrating the mechanisms involved.

Merely asserting it, or believing strongly, or ridiculing alternate caricatures, does not provide evidence for this belief.[/quote]
Yet, all you do is assert there is NO EVIDENCE!!! and play Christian martyr, all the while ignoring or finding ways to avoid having to admit there is evidence.

 

[Polymath257]

His posts literally contained LESS actual evidence and more of his own explanation than most of your opponents.

I just want to emphasize this. The difference, in addition to my being a mod, is that I ask what sort of evidence he requires as opposed to just giving it. At this point, that hasn't been answered.

 

[tas8831]

All that does is show BOTH dog breeds and wolves as tips of the canid tree.

Genetically, the wolf is the same as a dog. They can interbreed, which shows them as the same 'species', and they are similar both morphologically and genetically. There is more diversity among canids than most other haplogroups, yet they have not become reproductively isolated.

The condition of domestication is a man bred trait.. genetically, the wolf and dog are of the same haplogroup, or genotype. IOW, the wolf (many varieties) are just canids, like dogs. They descended from the same ancestor, and became morphologically homogeneous through man made or natural selection.

There is still a lot of variability within canidae, and new breeds (of all canids) continually present themselves. But the SOURCE of that genetic information is deep within the gene pool, and has limited presentation. .

"Because you can put together a graphical 'tree', showing plausibility of descent, does not provide evidence for descent. The conjectured graphic does not prove itself."

There is no mechanism to 'create' new traits. Only by 'selecting' the traits, can they become regular occurrences in the new clade or breed

What is your mechanism whereby all of the necessary alleles for each breed are held in check in the 'earlier' breeds that did not need them?

I mean, according to you, all such alleles are already there, created from dust of the ground somehow, just waiting to be 'needed' for the whims of desires of dog breeders.

What aspect of wolf anatomy or physiology 'contains' chihuahua traits?

 

[tas8831]

I just want to emphasize this. The difference, in addition to my being a mod, is that I ask what sort of evidence he requires as opposed to just giving it. At this point, that hasn't been answered.

And it won't be.

Ask him some more. You will not get it.

I cannot even get him to admit that he employs double standards when he wholeheartedly accepts the results of the Canid paper, yet summarily rejects/ignores papers showing the canids to be part of the Carnivora, or humans being primates, using the same type of data and the same kinds of analyses.
Not to mention that he claims analyses using mtGenomes use a "marker" to "trace" the "descendancy" yet cannot explain what "marker" he is referring to.

Soon, you will also be accused of slinging 'ad homs' and being a meanie..

 

[tas8831]

.

Show that any of the characteristics of modern dogs existed in the ancestral wolf population.

.that was the goal of the study.. to show actual descendancy, based on mtDNA evidence.

Same goal with this study:

A Mitogenomic Phylogeny of Living Primates

and this one:

https://pdfs.semanticscholar.org/23f2/2a07210a52dc49e0bdbdd97002fe21ea16a7.pdf

Yet you will reject them outright.

What are the "markers" you keep referring to? Specifics, please.

 

[tas8831]

I addressed the evidence of canidae in the earlier post. I'll make a few points afterward.


Quotes from the referenced study:.

Instead of searching for quotes that you can remove context from and declare victory, why not read the study to learn?

And again - this mtDNA "marker" you refer to is the entire mtGenome sequence. As indicated in the paper you enjoy:

" We sequenced the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes."

Pardon this "wall of text", but it is all from your Canid paper, and it shows that these "markers" you keep referring to are nowhere to be seen:

Previous studies have shown that domestic dog mtDNA sequences cluster in four main clades when compared with wolves, indicating different origination events (Vilà et al. 1997; Savolainen et al. 2002). In order to select samples of dogs representing several mtDNA lineages for the analysis, we sequenced the mitochondrial control region I for 88 dogs from 53 breeds. Among those individuals we selected 14 dogs, which included six from clade I (the clade that encompasses about 71% of today’s dogs; Savolainen et al. 2002) and two or three from each one of the clades II, III, and IV (Vilà et al. 1997). Because we wished to characterize mutations that occurred on dog lineages since the emergence of each clade, the dogs in this study were selected to be representative of the full genetic diversity observed in each clade (Supplemental Fig. S1). Complete mtDNA sequences, excluding the tandem repeat located inside the control region (Hoelzel et al. 1994), were obtained through polymerase chain reaction (PCR) amplification and sequencing. The complete mitochondrial sequence was also obtained for six wolves from throughout the world trying to represent as much of the previously described wolf diversity (Vilà et al. 1999) as possible: Spain, Russia, Saudi Arabia (two individuals), North America, and Sweden. Three coyotes (Canis latrans) from Nebraska and Colorado (two individuals), USA, were also sequenced and used as outgroups.

To construct a gene tree from the 23 complete mtDNA sequences, we first excluded the control region because of the high incidence of homoplasy (Ingman et al. 2000), resulting in a sequence length of 15,547–15,549 base pairs (bp). The average uncorrected pairwise sequence divergence between wolves and dogs was 0.47% (SE = 0.02), whereas average sequence divergence between coyotes and dogs plus wolves was 4.28% (SE = 0.11). A gene tree constructed with these sequences shows that all four clades of dogs are very well supported with bootstrap support values of 100% and Bayesian posterior probabilities of 1.00 (Fig. 1).​

and:

In order to assign nucleotide changes at each gene to specific branches and investigate their biochemical properties, we compared the maximum-likelihood reconstructed ancestral sequences at each node with those at neighboring nodes.​

These "markers"? Let me be generous here - THEY (if we are to consider snps 'markers') WERE ASSIGNED AFTER THE PHYLOGENETIC ANALYSES!!!

 

[tas8831]

Really? Show that any of the characteristics of modern dogs existed in the ancestral wolf population.

And he never did....

And he never will...

 

[Polymath257]

Directly from the canine study (in fact, the abstract):

"Here we show that dogs have accumulated nonsynonymous changes in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome. If this change also affected other parts of the dog genome, it could have facilitated the generation of novel functional genetic diversity. This diversity could thus have contributed raw material upon which artificial selection has shaped modern breeds and may therefore be an important source of the extreme phenotypic variation present in modern-day dogs."

Notice the phrases "elevated levels of variation", "novel functional genetic diversity", and "extreme phenotypic variation".

In other words, modern dogs show *more* diversity than the ancestral species. That is *directly* counter to the claims that diversity has decreased.

OK, so we have clear evidence *from the genomes* of the relevant species that dogs are *more* diverse than other species.

What evidence is there that diversity has *decreased* as opposed to *increased*, which is what this study supports?

/E: Also from the study:
"We hypothesize that changes in the living conditions of dogs as a result of domestication resulted in the release of selective constraint allowing a faster accumulation of functional (non-silent) genetic diversity in a large array of genes."

Notice that the variation has *accumulated* and was NOT there originally.

 

[Polymath257]

I addressed the evidence of canidae in the earlier post. I'll make a few points afterward.


Quotes from the referenced study:

1. It is remarkable that the potential for such large diversification existed in the ancestral wolf population.
2. Furthermore, the time since domestication seems insufficient to generate substantial additional genetic diversity.
3. Recent studies show that the origin of most dog breeds may derive from very recent selective breeding practices and are probably <200 yr old..
4. selection acts upon existing variability..

The diversity that was once in the ancestors of the canid line, has DECREASED, as each branch of the tree dead ends in limited diversity. Even contemporary wolves are tips of the branches, lacking the diversity the parent population once had.

This canid study is about mtDNA, but the FACTS about descendancy are plainly illustrated.

OK, let's try to understand exactly what is being said here.

What is the difference between 'potential for diversity' and 'diversity'? Let me give you an example.

Suppose a parent population has a single gene for some protein, and say it is

AGGACTCTTAGATTA

(I just made this up as an example). So, this is a sequence of 15 base pairs shared by *all* members of the ancestral population. The diversity of that ancestral population is low because they all share a single gene.

But, suppose that there are several viable mutations to this gene, say in positions 4, 6, 9, and 12. These mutations are not in the parent population, but are viable if selection pressures are different. This is *potential* diversity.

Now, in the descendant species, those mutations show up. So, the new species has variants

AGGTCTCTTAGATTA
AGGACGCTTAGATTA
AGGACTCTGAGATTA
AGGACTCTTACGTTA

Then, the *potential* diversity in the ancestral species has turned into *actual* diversity in the child species.

This deals with your comment 1. The paper is clear that the ancestral species had *potential* and that dogs have *actual* diversity.

Points 2,3, and 4 were addressed in the paper in the very next sentence. I quote:
"What is the origin of this diversity? We hypothesize that changes in the living conditions of dogs as a result of domestication resulted in the release of selective constraint allowing a faster accumulation of functional (non-silent) genetic diversity in a large array of genes."

In other words, the fact that dogs started living with humans made it so that selection pressures that existed in wolves no longer selected out those variants. This lead to increased diversity in the dog populations. So, again, they are very clear that the actual diversity did not exist in the ancestral population (because it was selected out) while the lack of selection pressures in the domesticated dogs allowed those mutations to stay fixed in the population. That lead to *increased* diversity.

So, your reading that the original population showed actual diversity is directly contradicted by the paper you refer to. Instead, it is clear that dogs have much MORE diversity than did the ancestral wolf population.

Is that more clear now?

 

[shunyadragon]

BTW, Poly, thanks for the civil, rational discussion. I was beginning to despair that to be possible in this environment!

The environment you yourself created.

 

[usfan]

..sorry. i haven't had time for forum debates, lately. I manage some properties and have had some emergencies that took priority over philosophical ponderings about our origins.
An hvac unit stopped working, and my servicewoman is gone for a week, so i had to get some portable ac units for backup. Then a sewer line backed up, i could not get it flowing, and had to meet a septic pumper to rectify the problem. A couple minor issues with a vacancy completed the time sink, and the forum was abandoned for more practical concerns.

Hopefully, i will get caught up, and will have more leisure time for delving into the mysteries of the universe..

The sewer line was a good reminder of how i am constantly dealing with other people's $hit, which is why I'm not phased by the poo flinging hecklers.


It's been over 100 for many days in a row, and the heat is draining. The monsoons are late, and every living thing is desperate for some rain. It's funny how dealing with the urgent necessities of life puts philosophical contemplation on the back burners.

Anyway, there are some good posts, and some snarky ones, that i hope to respond to soon.