Helpful Hint: If you put the title of the paper into scholar.google.com it will take you directly to the paper. Sometimes you have to follow a few links but I quite often find on-line copies of papers. Some that are quite old in fact.
Another thing to remember. Be careful of using just the abstract of a paper to determine what the research shows. If a paper is outside you area of expertise it is much better to work off of the Conclusion. I think abstracts were the first form of click bait. If you can’t get the actual paper it is safer to just ask if anyone has read the paper. I don’t know how many times I have read a YEC arguing using what was said in the abstract when the actual paper doesn’t support their argument.
Edit to add:
You might want to read the second paper returned by that search. It concerns a test for universal common
ancestry which, by the way, passes.
Apparently I missed the bulk of this platypus discussion - - but I do remember actually posting an image of one during one of my discussions with you.
And one teaching point you have been provided is that the various disciplines in Science are NOT over-turned by a single exception. Phlogiston (a theory for why things burned) was wrong for a century … REALLY wrong. And there were plenty of exceptions. But the pattern of exceptions was not enough to overturn the “Science” of Phlogiston until someone found a STRONGER pattern of what allowed for Oxidation.
Your statement that “nothing can overturn Evolution” is flatly wrong.
Scientists are not systematically stupid. Scientists are not systematically unfair. But Scientists are human.
No ONE thing is going to overturn Evolution or any other science. It takes a systematic pattern of errors that can be better explained by something else to overturn Evolution or any other science.
So… I’m going to cry fowl every time I see you trying to use a “single exception” as a valid way to overturn Evolution. It’s not the way science work… it’s not the way ANY science works.
Is there anything I have written that is not clear to you? Are you following my logic here?
Homologated cars don’t produce a nested hierarchy. Again, it is the PATTERN of similarities that evidences evolution, and that pattern is a nested hierarchy. We don’t see this pattern with designed things, only with evolved things.
Those are very different eyes. They are not homologous.
And they are very different eyes. First, the retina develops from different cell types. Second, the retina in the cephalopod eye faces forward whereas the vertebrate retina faces backwards. They are not homologous.
This overly brief discussion includes a test question:
“In a paternal family tree scheme does the top level, the father, consist of and contain the lower levels?”
[-] If you answer “yes” you are wrong.
[-] and if you answer “no” then you see why a paternal family tree is not a nested hierarchy.
Nested hierarchies are not tautological… they are different ways of arranging realities that can be used
to trace relationships. I’ve mentioned CSI scientists in courtroom settings several times to you. Nested
Hierarchies allow the application of logic to evidence in such a way as to determine what relationship one
branch of the hierarchy may have with another branch.
You need to provide a peer-reviewed article where a proven academic is agreeing with you about Nested Hierarchies. I’m pretty sure you will not find one credible article that discredits Nested Hierarchies - - because it is a part of the scientific process… not a lie-making machine to enable conspiracies of scientists around the world.
First, that paper from Sober and Steel isn’t about common ancestry per se. It is specifically about universal common ancestry and is focused on the base of the tree of life. This is clear to anyone who has read just the abstract. @Ashwin_s cites it and claims that it “voices the same concerns I also have” but it surely doesn’t. At least @Ashwin_s admits he didn’t even read it.
Followup to that particular paper has been modest (54 citations in 16 years, per Scopus) but the main answer to their question can be found in a 2010 paper in Nature, and discussion that followed:
Hi Bill,
There is a positive argument in 2010 by a guy called theobald… he was comparing universal common ancestry with specific ancestry (i.e he assumed evolutionary processes).
After his paper, there were a slew of papers starting from 2011, describing how his test had a selection bias towards UCA. The main author was a guy called T Yonezawa.
Anyway, thanks for the pointer on the other paper. I managed to get it. It does have an interesting statistical take on why it would be difficult to detect a common ancestor (more like LUCA).
Hi Marvin,
There is a third possibility.
If we view everything through the lens of evolution, there will be no way to falsify it.
Evolution and common descent are assumed beforehand in pretty much all these studies. So when scientists find out traits could not have evolved from a common ancestor, they assume it evolved parallely/convergently etc… And if nothing works, they claim horizontal gene transfer.
So we get scenarios like the appendix evolving 32 times etc.
This is why I never expect biology to falsify evolution.
Did you read that paper? I just did. It’s about when and how to use the UCA test. It’s not about whether common ancestry is true. Check out the last two sentences.
But this is all beside the point. This strange part of the thread started with the citation of a paper by Sober & Steel that you didn’t even read but which you portrayed as casting doubt on common ancestry. That’s really, really far off.
The subject of the paper you cite is whether the hypothesis of universal common ancestry is supported by the 2010 Bayesian analysis performed by Theobald, et al. If you think that this undermines the phylogenetic tree of mammals and reptiles, methinks you have misread the paper.
From the conclusion:
We want to emphasize again that we are not denying the common ancestry of the data set analyzed in Theobald (2010). What we and others have been pointing out are shortcomings of the UCA test itself.
Yes, . The conclusion from the study he showed was not questioned (i.e whether UCA happened or not). However, it was observed that the method used created false positives of lineage due to selection bias.
@pevaquark:
Like i have said n no: of times, genetic analysis assumes common ancestry. So if common ancestry is possible, then if genes are similar, they are labelled as homologs.
If not, they are thought to arise from vconvergence. There is no sure fire way to test whether this is actually true.let me quote:
Blockquote
So how can one decide what family a given protein belongs to? Sequence analysis aims at finding important sequence similarities that would allow one to infer homology. The latter term is extensively used in scientific literature, often without a clear understanding of its meaning, which is simply common origin. Since the mid-19th century, zoologists and botanists have learned to make a distinction between homologous organs (e.g. bat’s wing and human’s hand) and similar (analogous) organs (e.g. bat’s wing and butterfly’s wing). Homologous organs are not necessarily similar (at least the similarity may not be obvious); similar organs are not necessarily homologous. For some reason, this simple concept tends to get extremely muddled when applied to protein and DNA sequences [695]. Phrases like “sequence (structural) homology”, “high homology”, “significant homology”, or even “35% homology” are as common, even in top scientific journals, as they are absurd, considering the above definition. “Sequence homology” is particularly pervasive, having found its way even into the NLM’s Medical Subject Heading (MeSH) system. It has been assigned as a keyword to more than 80,000 papers in MEDLINE, including, to the embarrassment of the authors, most of their own. In all of the above cases, the term “homology” is used basically as a glorified substitute for “sequence (or structural) similarity”. All this misuse of “homology”, in principle, could be dismissed as an inconsequential semantic problem. One could even suggest that, after all, since it so happened that in molecular biology literature “homology” has been often used to designate quantifiable similarity between sequences (or, less often, structures), the term should be redefined, legitimizing this usage. We believe, however, that the notion of homology is of major fundamental and practical importance and, on this occasion, semantics matters. In our opinion, misuse of the term ‘homology’ has the potential of washing out the meaning of the very concept of common evolutionary descent [695]. A conclusion that two (or more) genes or proteins are homologous is a conjecture, not an experimental fact. We would be able to know for a fact that genes are homologous only if we could directly explore their common ancestor and all intermediate forms. Since there is no fossil record of these extinct forms, a decision on homology between genes has to be made on the basis of the similarity between them, the only observable variable that can be expressed numerically and correlated with probability. The higher the similarity between two sequences, the lower the probability that they have originated independently of each other and became similar merely by chance (see 4.2). Indeed, if we take two sequences of 100 amino acid residues each that have, say, 80% identical residues, we can calculate the probability of this occurring by chance, find that it is so low that such an event is extremely unlikely to have happened in the last 5 billion years, and conclude that the sequences in question must be homologous (share a common ancestry).
Blockquote
Blockquote
Why is sequence and structural similarity considered to be evidence of homology (common origin) in the first place? Once we are confident that a particular similarity is not spurious, but rather, according to the above criteria, represents certain biological reality, is common ancestry the only explanation? The answer is: no, a logically consistent alternative does exist and involves convergence from unrelated sequences The functional convergence hypothesis would posit that sequence and structural similarities between proteins are observed because the shared features are strictly required for these proteins to perform their identical or similar functions.Functional convergence per se is an undeniable reality. In the broadest sense, convergence is observed, for example, between all proteins that contain disulfide bonds stabilizing their structure or between all enzymes that have the same catalytic residues (e.g. a constellation of histidines and aspartates). Even more prominent motifs associated with catalytic residues are found within different structural context and, in all likelihood, have evolved convergently [722,724]. In the case of disulfide-bonded domains, convergence can even fool sequence comparison programs, translating into statistically significant (albeit not overwhelming) sequence similarity. A rather dramatic manifestation of convergence is the recent description of a “homologous” disulfide-bonded domain in Wnt proteins and phospholipase A2 [699], which was later recognized as “mistaken identity”, on the grounds of structural implausibility [77]. The classic work of Alan Wilson and colleagues comparing lysozymes from ruminants, langur monkeys, and leaf-eating birds is a textbook case that reveals the nature and extent of convergence in enzymes [471,806,816]. These studies have shown beyond doubt that several amino acid residues required for functioning in the stomach have evolved independently (convergently) in different lineages of lysozymes. Importantly, however, this set of convergent positions consists of only seven amino acid residues, a small subset of the residues that comprises the lysozyme molecule.
Blockquote
Source:Evolutionary Concept in Genetics and Genomics - Sequence - Evolution - Function - NCBI Bookshelf
In conclusion, two genes have a common ancestro when they share statistically significant similarity… unless of course they dont have a common ancestor. In which case, the similarity is due to convergent evolution.
i.e as far as genetics vis a vis common ancestry is concerned. Genetic similarity is a tautology. Ca is shown by similarity… Ca is shown by less similar genes… And Similar genes might not share a CA…
If its a coin toss experiment, it would go like this. If its head: CA happened.
If you get Tails: Then also CA happened.
If the coin didnt fall down… CA happened.
Reality has a way of poking through our chosen lenses if those lenses are so wrong about things - especially when our lens is so widely shared among so many who continue to probe into that reality (i.e. – the opposite of isolationism). This is why those who wear the lens of a “young earth” (I know --that does not include you) have not been able to maintain that lens, except among their own isolated groups. And yet there was a day when everybody thought that way – the lens should have been invulnerable to any falsification on your reading of how this works. It wasn’t. There were just too many places reality did not conform for that lens to remain viable.
It may well be true that much of biology presupposes C.A. today in order to build toward other conclusions, just as astronomers [now] presuppose that the earth moves around the sun. They do so because it continues to work and be fruitful for more detailed understandings.
Here is the situation I’ve been observing (and not just with you but with how these exchanges have gone without any exception that I can think of): scientists have been building an edifice – always incomplete of course, but slowly adding things to it. Some members fall off or don’t last. Other members do last, and yet the edifice while impressive always has more needing to be done. Challengers like yourself to certain [now foundational] parts of this edifice come along and attempt to point out problems with it. And many times these alleged problems aren’t really problems at all but have been amply answered. Other times you may be correct that something just “isn’t there” yet --maybe there is a certain type of fossil that actually does still remain to be found. But here is the general observation that interests me.
These exchanges have this one commonality if we see this as a conversation between the “builders” (scientists) and the “critics” (in this case you).
Critic: “Your house has problems X, Y, and Z – the foundation must be bad.”
Builder: … explains why X, Y, and Z either have already been thought of and answered … or else we expect they soon will be. …“and besides, here is our standing house, such as it is thus far. Can you, Mr. Critic, offer a better working foundation for us to try?”
Critic (ignoring the last question): “No – but you don’t understand. If your foundation was really valid, then X, Y, and Z would not be problems for you. You’re just using a presuppositional lens that causes you to ignore these problems.”
Builder: “Well, X and Y aren’t really problems. As we keep telling you, X is just a dishonest misreading of this literature, Y has been amply answered, and Z is still an interesting matter of investigation. Besides, if our foundation is so problematic, why is there this standing house here?”
Critic: (Ignoring the last question) “Of course you think you’ve answered X and Y because you go into your investigations assuming your foundation works. And you still haven’t answered Z, and for that matter a,b,c, and d.” (still missing upper stories of the house that aren’t complete.)
Builder: “Well, I guess you’re entitled to think that way. But if our foundation is so untenable, you still haven’t explained how we already have so much of this successfully standing house here before us.”
Critic (wishing he could just ignore this singular challenge) “But it isn’t successfully standing! It’s been falling over and is about to crumble at any moment!”
Builder: “Well, you and a lot of variously motivated others have sure been trying your hardest to knock it over! For something you allege to be so fragile, one would think we would all need to be tiptoeing around lest it fall. You’ve been far from alone in stomping all over this foundation. Other than a few problematic parts that have now been culled away, the core still looks to be solid. The house is … still standing after all.”
This is how all these exchanges always go, pretty much without exception. One side declares that it doesn’t work. The other side patiently and educationally explains exactly why it can and does [or plausibly could] work. The education and growth of understanding is disproportionately present on the latter side, while the former side’s main [only?] contribution is to attempt to cast doubt. This, more than anything else, is what persuades me that the ideological critics have so far failed to be compelling.
@Ashwin_s I don’t want to have to go back through your 88 posts so let me just ask you straight up, What is your position? It appears to be Old Earth/ID/progressive creation. Am I correct?
The reason I ask is I don’t understand why someone who affirms ID would argue against Common Ancestry. After all Common Ancestry could be called Common Design.
If the house you are referring to is the tree of life, it’s full of imaginary creatures at its node.i.e-The alleged common ancestor.
It’s a strange creature in the evolutionary tree… sometimes real, sometimes imaginary… when scientists make stories/hypothesis etc ,they are real creatures with real traits… however when it comes to actually identifying them… They are imaginary, non existent constructs.
It’s like showing a couple of doors, windows, and a very small no: of bricks lying on the floor and claiming it’s a house.
As to astronomers assuming the earth revolves around the sun… There is real physical evidence for the sun and the earth(The only assumption involved is that reality is real). Its a real time measurement.The Common ancestor is a much more elusive animal…
Even in evolutionary terms it’s real as well as imaginary.
And you can’t really falsify Such a creature. Nothing to test against!
For example: to verify whether genetic predictions of lineage are true. We need the genetic sequences of the common ancestors/intermediate species… How do you verify something like that?
But what we can ask ourselves is: “What would we expect to see, if this immensely long history of life and death is true?” Of all the millions of species through history, what percentage of those could we expect to be found and catalogued? Given that so many of them would be destroyed without leaving fossil trace, and given that we can only search a tiny percentage of the earth’s surface, it is pretty impressive to me that we have as many as we do.
As to “the common ancestor” – I take it that you are referring to the one trunk of the tree at the very beginning. You realize this butts up against abiogenesis, don’t you? It would be impressive indeed if we had solved those mysteries all the way back to what that must have looked like. It’s being worked on, to be sure. But beyond knowing that it was something “simple” (like a single-celled organism) or something that had reproductive capability (and granted – that is far from simple as we can now see), this is still a mystery. And that it is so does not really surprise us.
One thing I did not mean to decry in my imagined “conversation” of the last post is skepticism or criticism, even though it was cast in an almost consistently negative light there. The skeptics and critics, whatever their motivations (ideological or not) are a valuable part of the whole process. And in the past they have sometimes prevailed over long-standing edifices (like geocentrism).
In my archetypal conversation, my own pointed criticism is aimed at the critics who, because their ideological motivation is so strong, even lapse into self-deception over matters that have reasonably been addressed. And in turn they deceive others with mistaken appraisals over the true state of affairs.
One difference I see between today’s scientific “edifice” (whether it be an impressive multi-storied building or a humble few scattered bricks as you suggest) is that skeptics today (unlike back in geo-stationary times) have much more powerful tools with which to challenge potentially weak foundations. Courtesy of well-developed scientific methodologies, today’s critics have jack-hammers whereas many centuries ago, they had little more than sticks comparatively speaking. And those were only in the hands of a tiny few who had the luxurious leisure to go poking around at such things. That they managed to topple long-standing assumptions was an impressive and hard-won feat. In contrast, anything that survives today’s skeptics with their scientific and communication tools has to be impressive in its own right.
No it doesn’t. Not one bit. It is a testable idea. For example, this paper which was discussed extensively over in the recent ERV thread found that the class of retroviruses were inserted exogenously (i.e. the genome was bombarded by viruses so to speak) as opposed to through common descent. Some of their reasons were related to the fact that less than 5% of the viral insertions were at homologous spots in the genome. What we see with common descent is 99.9%+ of viral insertions at homologous spots in the genome as is the case with humans and chimpanzees. The notion of common descent is NOT assumed but is TESTABLE.
I’ve also said this before: genes are much much much much more similar than they need to be if common descent is false. I shared a snippet of 90 base pairs that had over 53 million ways they could be arranged and have the exact same function!!! I think that we should start with some basics again for how anyone tests common descent from any genetic analysis through this useful analogy of how we read and analyze ancient texts:
No. No. and No. How about this analogy instead.
If its a coin toss experiment, it would go like this:
If it’s heads: God supernaturally intervened and we will have no natural explanation ever.
If its tails: God supernaturally intervened and we will have no natural explanation ever.
If the coin didn’t fall down: God supernaturally intervened and we will have no natural explanation ever.
You quote mined the authors. It is interesting that you didn’t quote this part: This view of evolution is clearly inferior to the alternative, whereby all significant similarities observed within a class of proteins are interpreted within a single theoretical framework of divergence from an ultimate common ancestor.
The first thing to do is to compare the function of an organ in two species, and also look to see if the organ has adaptations that have been selected for. Obviously, the limbs of a tetrapod are adapted to movement on land, so that is why they are not vestigial fins. They are adapted fins. The human caecum has nearly disappeared, and the main part that remains is the appendix. The human caecum has not kept the same function as seen in ancestral populations, and there has been no selection for an equally vital and different function. What is left is a rather rudimentary and non-vital function of housing some gut flora that may help to repopulate the gut at a later date which is tiny function compared to the function of digesting cellulose in other species. It is entirely possible that mutations to the caecum will add important function in the future, which is why the caecum can enlarge and shrink through time in a lineage.
Part of the confusion is that there are really two arguments when it comes to vestigial organs. The first argument is an aesthetic one. Why would a creator include such a kludgy organ in the design of an organism? If whales were created as whales, why include all this stuff from terrestrial mammals, like a vestigial pelvis for walking on land?
The second and non-arbitrary (i.e. scientific) argument is a phylogenetic one. These organs follow the expected phylogenty. We find vestial mammal features in whales because they descended from terrestrial mammals. We don’t find vestigial bird features in whales, as an example. Whether these vestigial organs turn out to be important or not, it really doesn’t matter. The evidence is the phylogeny, not our judgement of how useful they are.
If you can’t get the actual paper it is safer to just ask if anyone has read the paper. I don’t know how many times I have read a YEC arguing using what was said in the abstract when the actual paper doesn’t support their argument.
