Common Descent Cladograms are all Fake, Convergent Evolution Explains Everything

I’m sorry. You think that this isn’t explained? What about even granting something as basic as this:

Tadaa, a variable like height changing all the time. Or the spleen story:
http://www.sciencemag.org/news/2018/04/indonesian-divers-have-evolved-bigger-spleens-hunt-underwater

Evolution doesn’t explain this very well? Holy cow. I’m going to have to call this effect occurring here as again, you are demonstrating that you do not understand evolution at all:

Here are a few basic thoughts…

Eyes are good. Organisms tend to keep them once they begin evolving. No need to change them around. Our eyes are messy byproducts of many generations of eyes.

Generally organisms tend to be more stable if their evironment is stable. This is why you tend to see a lot of change occuring with dramatic changes in the environment.

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The analysis does not prove. It speculates. There is a difference…

To be specific it speculates that the fossil skull of an organism thought to exist 36mya is an intermediate between pakixetus and aquatic whales.

For it to influence the whale lineage, it has to predate it!.. and there is now evidence it does.
I could make a story that whales are directly descendant from amniotes and the all the interim forms are cetaceans “evolving” back to become land living organisms…
The same evidence/clades could be used to prove this…

The hypothesis is highly speculative… and add to it that there should be many many more “interim” fossils… thousand of them… but we can’t find any…

And whale evolution is the case study with the best evidence!

They aren’t the same genes. They have different sequences.

There are different eyes in different lineages. They are as different as a bird wing is to a bat wing. Why would a designer design a different eye for different groups of animals? Why are specific eye designs specific to one lineage? That doesn’t make any sense for intelligent design, but it makes completely sense for common ancestry and evolution.

Again, adaptations stay specific to a lineage. That’s how evolution works, but that is not how design works. This is why a nested hierarchy falsifies design and supports common ancestry and evolution.

A designer can mix and match parts however the designer wants. This is why we observe that designs do not fall into a nested hierarchy.

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No, you don’t. This is illustrated by this statement:

" If there are ten, variables in a product/process. Then if some of the variables, say three are kept constant without change, and incremental random changes are made in the other 7, you will get a nested heirarchy with the point of similarity being the three variables being kept constant.(the technical term for this is restricted randomisation)."

That’s now how nested hierarchies work.

I already demonstrated that this is false.

Let’s use your example and see how it works. Let’s use mammals and birds and see if it works.

The three features we will keep the same are a backbone, four limbs, and a cranium.

To keep things a bit more tidy, we will have three features that mutate randomly which are mammary glands, feathers, and middle ear bones.

Species A: mutated three middle ear bones, mutated feathers, mutated mammary glands.

That species would easily violate the predictions made by the theory of evolution. That species would falsify common descent.

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@Ashwin_s

I believe @T_aquaticus has done an impressive job showing your understanding of Cladograms and your analysis of a professional’s analysis is completely “wanting”.

As to this old “card” that there should be more “interim” fossils… the term is actually INTERMEDIATE forms… or, the term Transitional was used in prior years, but leading to disputes about what exactly “transitional” means. But there has been a general move to replace Transitional with Intermediate.

But in reference to your objection about how few there are … there ARE many many more intermediate forms… which are not necessary for the purpose of this analysis. You really are a pip…

@Ashwin_s,

I have been discussing your situation with some of the moderators. I spoke with @pevaquark and have invited @T_aquaticus to review my comments. BioLogos, unlike so many of the Creationist and I.D. blogs/sites/lists, is painfully open to folks like you coming in and discussing whatever they want to discuss.

And the BioLogos volunteers/supporters, like me, and even the moderators (who are also volunteers), frequently want to help convey information on Evolutionary principles to critics of Evolution … or sometimes we want other participants to see and read what we think are relevant thoughts regarding questions, whether newly formulated or “old standbye’s”.

I’m going to offer you a great deal.
You have received considerable time and attention … and clearly it is an indication of the generous spirit of the Moderators and others to give you so much of their time. But I have also read, frequently, that you may be pretty much ignoring all this information. Sometimes this is an unintentional result of the stress and demands of thinking through what can be complex Evolutionary scenarios. But other times it seems like some critics just have no intention of accepting anything a scientist says… or accepting anything a pro-Evolutionist might say.

I don’t think you fall in the latter category. So that’s why I am going to offer you this deal.
If you can name the three most significant things you have learned about Evolution from the kind efforts of @pevaquark and @T_aquaticus, I will continue to field your questions for another week or more.

When I use the term “significant”, I don’t mean something that has to be earth-shaking, or a proof. It can be something that you had never thought of before, even a little thing. But if you could come up with three things you learned… three things you wouldn’t have known if it wasn’t for these collegial volunteers, I will take a deep breath and come back to these discussions with a fresh view and a better outlook on where the discussions are going… even if they don’t really seem to be going anywhere. I’m just a volunteer like so many others on this list… but I would like to tie my continued efforts to some tiny sense of progress that we think we are making by fielding questions on Evolution from all over the map.

If you really can’t think of three things … then, that’s okay too. But I’ll have to be moving on to some other matters. I trust you will understand. Please advise. It will be very interesting to read what you have to say.

Although my expertise isn’t in mind reading, if I were to guess I would say that the major hurdle is in understanding that transitional and ancestral are two different things. A transitional fossil is never claimed to be a direct ancestor of any living organism, or at least they shouldn’t be claimed as such. A transitional fossil is simply a fossil with a specific mixture of features. Nothing more. Nothing less. One could argue that a platypus is a transitional species because it has a mixture of reptile features not found in placental mammals and mammal features not found in reptiles. No one is saying that the platypus is our ancestor, but it is still transitional.

Also, one doesn’t have to assume that a transitional fossil is an ancestor of any living organism in order for a transitional fossil to be evidence for evolution. You don’t have to assume anything about the fossil other than it is a rock that preserved the shape of a dead organism. If we found transitional fossils that had a mixture of bird and mammal features this would falsify evolution, as discussed before. It is the mixture of features in fossils that allows us to test common ancestry and evolution because those concepts make very specific predictions about what mixtures of features we should see and which we should not see.

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My dear friend they are as similar as genes which are considered homologation.

Whoever told you this spoke a half truth. Very often in genetics, the difference between homoplastic and homology is the faith of the scientist…the lens in eyes are different. However, many of the Gene complexes are very similar.

Blockquote
Did the diversity of lens-containing eyes evolve from one ancestral eye (monophyletic evolution) or from multiple, independently derived eyes (polyphyletic evolution)? Monophyletic evolution would make diverse eyes homologous (inherited similarities from a common ancestor); polyphyletic evolution would make eyes homoplasious (independently acquired similarities). Historically, anatomical and developmental differences among eyes of different species favored homoplasy; however, recent molecular data indicating that all eyes employ a similar cascade of transcription factors (proteins regulating gene expression) for development have suggested homology.
Blockquote
http://m.genome.cshlp.org/content/14/8/1555.full.html

Recent studies also show that the gene pathways/ expressions for the camera eyes of human and octopus are similar…they share around 69% of the genes.

Blockquote
Our results indicate that most of the genes, including several gene pathways necessary for the evolution of the camera eye, might be shared between human and octopus lineages. Therefore, there is strong evidence that the evolutionary mechanisms for the camera eyes of humans and octopuses are subjected to similar gene expression profiles of the commonly conserved gene set, although the developmental processes of the human and octopus eyes are a bit different. We believe that these gene expression similarities could be the bridge of understanding from the genetic system of eye evolution to the developmental process of the camera eyes of humans and octopuses
Blockquote
Source:http://m.genome.cshlp.org/content/14/8/1555.full.html

Blockquote
Using the 1052 nonredundant sequences from the octopus eye as query sequences, we performed a BLAST search against the 13,303 human genes. As a result, we identified a total of 729 genes that were commonly expressed in both human and octopus eyes (Fig. 3). It follows that 69.3% of the 1052 nonredundant sequences from the octopus eye were commonly expressed in the human eye. To test whether these genes are significantly different when the same sequences from the octopus eye are compared with the genes expressed in human tissues other than eyes, we also performed a homology search between octopus-eye ESTs and human-connective-tissue ESTs. To be fair, we used 2430 human-connective-tissue ESTs as well as 3809 human-eye ESTs from the same database, BodyMap. We then found that the number of genes commonly expressed between the octopus eye and the human connective tissues was only 44, whereas that of genes between the octopus and human eyes was 162 (Fig. 3). Thus, the former was about four times less than the latter.
Blockquote
When you do homology searches using BLAST programme, examples of “convergent” evolution are also shown as homologous.

This is magic talk. The first mammal is supposed to have evolved 160mya. We see all kinds of diversity in extant mamamls such as flying mammals, aquatic mammals, mammals with external placenta etc. They have gained as well as lost adaptive features throughout. Yet somehow there is a rule that some specific adaptations such as hair stay conserved???
That’s nonsense.

Edit: highly conserved elements coupled with diversity forming nested heirarchies of mechanisms occupying different niches in terms of function is a hallmark of design actually. All know designed products show this quality.

Why don’t you tell me how it works…
This is exactly how nested heirarchies arise.
This is done very often in design of experiments to get a nested heirarchy or experiments.

I don’t know if you are being serious. Mammary gland and all are not variable. Variables are root factors which can change the mammary glands like the genetic code/gene regulation mechanisms etc.
We are talking about millions of variables interconnected to each other. Out of these, some variables need to remain constant expressing the same morphology/function.

Going to pop in with this constantly growing series (now 5 hrs+) on the systematic classification of life and there is lots and lots of nice information on many different phylogenies:

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Brooks, I have a job. And it takes some effort from my part also to share the things that I do.
I have replied as consistently as I can. It’s true I might have missed replying to some articles. For example @pevaquark, sent a beautiful diagram of whale evolution. I asked him for the source, I didn’t see any response. So I searched for the background and found a similar drawing in the Berkeley site. The source for this drawing seems to be a paper published by Thewissen et al. There was a subsequent paper submitted by Gayle et al describing variants of the same diagram.The main thrust of @pevaquark’s argument was that phylogenies are substantiated by the fossil evidence and this proves evolution. The problem is that as per Gayle et Al, these trees are informed significantly by fossil morphologies. So there should be nothing amazing about the tree reflecting fossils. And hence the argument is circular. I have made this point to many people.And I didn’t get the time to write a reply to @pevaquark… and then replies mounted up and I forgot to respond.
I suggest all of you read my response to the others also to get a clear picture. I can’t keep typing the same thing again and again.
Three things I learned as a part of your replies/researching claims made are as below-

  1. Evolutionary biologists seem to seriously believe that incremental changes lead to nested heirarchies. I learned that you need carefully regulated change to bring about nested heirarchies. I came across a useful paper in design of experiments explaining how this process creates nested heirarchies and my understanding is solidified.(A good example in nature is the development of embryos).
  2. I learned that one of the basic assumptions of cladistics is common descent and bifurcation. Which helped me understand why scientists ignore the possibility that common descent did not happen when they engage in these activities and present spectacular hypotheses such as the appendix convergently evolving 32 times among mammals with a straight face.
  3. I learned about the importance of fossil morphology in the analysis for fixing lineage. As per scientists, the morphology of fossils tell us more about lineage than that of extant species (This is again because of asssumig common descent).And hence, things like a ear bone in a pakicetid tells us more than echolocation shared by whales and bats… It’s circular reasoning as far as I can see.
  4. Also a lot of questions have popped up in my mind which I am planning to investigate when I have time… like below-
    a) is antigen formation in the human body an example of a design of Experiments?
    b) If evolution is true, what could be the nature of the regulatory framework which leads to nested heirarchies.
    I don’t know if anyone is researching along these lines. But I will find out what I can.
    I appreciate @pevaquark @T_aquaticus @Bill_II et Al for your efforts.
    How you run biologos is totally up to you. However I would expect every discussion to be a two way thing.
    If you don’t like these kind of discussions, pls make it a policy to kick out people who ask questions…
    That’s a policy decision you guys need to make.

Did you read the original article on this one? For those interested, there’s a very readable (and very interesting!) abstract here: Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes - PMC. I’m not a biologist, but I followed most of it (edit: most of the abstract, that is! :slight_smile: ) pretty easily.

The findings of this article are actually perfectly consonant with standard evolutionary theory, of course. Essentially, therian (non-monotreme) mammals all have XX/XY for their sex-determining genes. Other vertebrates have different systems, though. How did XX/XY come about, then, in the grand natural history of genetic development? A fascinating question. They looked at monotremes, who are intermediate forms between mammals and other vertebrate families, and found that the X chromosome in the crazily weird monotreme XYXYXYXYXY system actually bears no resemblance, on close analysis, to the X in the therian XY system but it is rather closer to the Z sex-determining chromosome of a chicken. There are surprises here, sure, but nothing controverting the standard model of mammalian emergence in natural history or the origins of the platypus.

What seems sort of disingenuous in your presentation of these data, Ashwin, is that you imply that the chromosome is related specifically to bird sex chromosomes, to the exclusion of others. As I’m sure you realize, that’s not actually what the authors show. The only genome they worked with outside mammalia was the chicken’s. They specifically state in the “for future research” bit of their conclusions that

The imminent accessibility of the complete platypus genome, the ever-growing genome data in a wide range of taxa, and future comparative gene mapping, notably involving reptiles, will test the significance of the monotreme sex determination system and will provide further insights into sex chromosome evolution in vertebrates.

In light of this, brother Ashwin, do you really think this is a significant anti-evolutionary finding?

I leave you with one of their more interesting figures from the paper, along with a sincere expression of my gratitude for introducing me to this fascinating study. (See original, zoomable version here.)

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I’m not insulted, George. I’m merely trying to show that certain types of reasoning we commonly find in creationist apologetics seem silly when applied to other fields. “They believed X… now they believe not-X! And both are consistent with evolution! It’s unfalsifiable!” Well, no, first you actually have to show that X-versus-not-X was something that would have falsified the theory in the first place. Typically, nobody bothers to try and prove that. Rather, they’re satisfied to score rhetorical points by calling something “unfalsifiable,” ergo “nonscientific,” ergo “false.”

There is no contempt involved. Yes amount of bewilderment and disappointment.
It’s kind of strange, when people like me point these things, we are not trained…
When guys with PHDs such as Dr Jonathan wells do it, they are called biased…

I’s biological training a code for indoctrination?

It’s because I am not an expert in this field that I have backed up each one of my claims with reference to peer reviewed and published papers.
By the way, I am not the only one saying common descent is almost universally assumed and hardly tested. Let me point to another paper… Unfortunately I am able to access only the summary.

Source:https://www.researchgate.net/publication/11077157_Testing_the_Hypothesis_of_Common_Ancestry

Blockquote
Abstract
The hypothesis that all life on earth traces back to a single common ancestor is a fundamental postulate in modern evolutionary theory. Yet, despite its widespread acceptance in biology, there has been comparatively little attention to formally testing this “hypothesis of common ancestry”. We review and critically examine some arguments that have been proposed in support of this hypothesis. We then describe some theoretical results that suggest the hypothesis may be intrinsically difficult to test. We conclude by suggesting an approach to the problem based on the Aikaike information criterion.

Testing the Hypothesis of Common Ancestry | Request PDF. Available from: https://www.researchgate.net/publication/11077157_Testing_the_Hypothesis_of_Common_Ancestry [accessed Jun 19 2018].

Blockquote

Though I couldn’t access the paper, it voices the same concerns I also have.

Hi,

I wasn’t misrepresenting anything (at least I didn’t intend to). I try to give my source clearly to ensure transparency.

If you read the abstract I quoted, it says clearly the Sex chromosomes are related to mammals… and birds…
It’s basically all over the place and that’s problematic.
Or at least it should be according to the falsifiability criteria discussed with @gbrooks,@pevaquark,@bill_II etc…

Its definitely a fascinating study. :slight_smile:

I honestly appreciate that. Some people come in here with heresay. You at least come in with scientific studies to discuss. One thing that would have helped in this case was an actual link… but anyway, Google provided it for me with a couple more clicks, no harm done.

The authors were using the word “birds” to refer to the fact that they had compared mammal chromosomes with the chromosomes of a chicken. If I may be so bold as to exegete Veyrunes et al., “bird” was a shorthand for “non-mammalian vertebrates, as represented in our study by chickens.”

It’s all over the place, but it’s not the least bit problematic. As mammals emerged and diversified, (God working through) evolution eventually settled on an XY pattern for sex differentiation. This is the consistent pattern throughout the therian (marsupial & placental) line. Along the way to this, it apparently went through a series of intermediate stages, one of which was the platypus model, which still in part resembles non-mammalian vertebrate chromosomes.

What do you think I’m missing here? What of this seems to you to falsify evolution?

I am not claiming it falsifies evolution. I have always said nothing will.
Friends here pointed out that features of birds in mammals will falsify common descent…
Hence I pointed to the platypus and asked whether it will. (In addition to the sex chromosome similar to chicken, it also has micro RNA similar to chickens, and egg yolk protein found in birds and fish.)
All this indicates that the platypus (a primitive mammal) had an ancestor that predates sauropsids(the ancestors of reptiles)…
This leads to problems because evolution is supposed to happen step by step. So scientists had proposed mammals evolved from mammal like amniotes called synasids…
And reptiles from amniotes with reptilian traits called sauropsids.

Now, however, because of the platypus, there is a mixed bag common ancestor with primitive mammalian, reptilian and chicken like features… This should have thrown a lot of evolutionary stories for a toss. Surprisingly, it didn’t…
I don’t know why.

@pevaquark,@bill_II,@gbrooks9
I think this should end the debate on whether fossils with mixed features would falsify evolution…
It will not.
https://www.nature.com/news/2008/080507/full/453138a.html

Edit: Spelling of sauropsids corrected.

There are at least two important senses in which something may in the end prove non-falsifiable:

1> because it problematically falls short of being a good scientific claim (e.g. ‘Last Thursdayism’ – in which the world and people in it were all created a week ago with false memories and false appearances of age)

2> because it turns out to be true (e.g. that the earth actually moves around the sun and turns around its own axis.)

Both of the above seem to us at the moment to be stubbornly immune to falsifiability. You latch onto the first option, of course, but seem unwilling to ever consider the 2nd.

Evolutionary theory is a broad body of work that is pliable, and adaptable (within limits!) to new data that comes along. Some see this as a strength; others like yourself interpret this as an infinite adaptability that carries it all the way into the realm of being non-falsifiable.

It seems to me as an outsider to the life-sciences, as if the latitudes for adaptability have been sharpened down significantly over the last century (and even decades). I.e. There are probably more ways to falsify it now than there used to be. Don’t ask me to specifically name one – I’ll leave that to others here more knowledgeable in genetics and such. But the overall theory seems to have been refined considerably and with much fruitful inquiry. You perennially tout that as a weakness – even all the way to an accusation that it can’t be falsified. But it seems to me that this is its strength – and that in the sense of the #2 option above.

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Hi Ashwin,

Actually, I’ve read the paper and it doesn’t. Here’s an extended quote from the conclusion:

We hope that biologists will use the protocol we have described for different sets of species. It may turn out that all is well with the conventional wisdom on this subject. What Crick defended by considering a single characteristic–the genetic code–may be vindicated when one considers sets of characteristics whose functional significance is less well understood. But perhaps it will emerge that for some groups of species, the data do not provide unambiguous support for the idea that there is a single common ancestor. [Emphasis added]

The question being asked wasn’t whether the phylogenetic tree of mammals and reptiles is reliable (it is); it was whether the tree that includes every form of life on the planet can be traced back to a single root, rather than a bush, at 3.5 bya. The paper notes that Crick’s inference of a single root of common ancestry from a single genetic code is valid; but suggests that, with the advent of relatively inexpensive DNA sequencing, more evidence can be analyzed. The paper notes that one possibility would be the discovery of an uncertainty boundary somewhere in the deep past that could not be traversed by comparative genomics; the other is that single root common ancestry would be more strongly supported. In either case, the paper urged more research to see what the evidence would turn up.

Here is a link to the paper so you can read it for yourself, Ashwin: http://courses.botany.wisc.edu/botany_940/06EvidEvol/papers/Sober&2002.pdf

Our friend @sfmatheson has tremendous expertise in the biology literature, so perhaps he would know of any relevant papers that have been published in the 16 years since this one. Do you know of anything, Steve?

Yours,
Chris

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@AMWolfe

So… a Creationist, in attempting to show the limits of human science, might argue that
“calling Pluto a planet or a dwarf planet is another example of scientific claims that can’t
be proven false”, right?

And since that is frivolous claim, we can defend against some parallel charges against Evolution
by pointing out that “said YEC” is disputing a “classification issue”, rather than an actual
Scientific conclusion.

Do I fairly capture the essence of your last posting?