Whales did (NOT) evolve


(Chris Falter) #185

You keep repeating this same incorrect assertion, Ashwin, even though the actual facts have been pointed out to you already. For example, 3 weeks ago:

You tried to rebut this by citing a paper, but unfortunately you greatly misread it. Let’s examine a statement from the paper you cited:

Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea .

As we see in the paper itself, the molecular datasets yielded–drum roll, please–trees.

Just like trees built from fossil evidence, these trees contain branches along the path from a common ancestral population to the modern leaf nodes, which are extant populations.

Dennis Venema wrote a very helpful article on how genomic evidence yields nested hierarchies. I offer it for your edification.

Grace and peace,
Chris Falter


(Lynn Munter) #186

Maybe you are not aware that although “all existing classification” was first based on phenotypes (and for most fossils it still is), then scientists went through and independently made classification trees based on genotypes, and with very minor modifications to the phenotypic tree, guess what? They matched up really, really well!

It’s a common misunderstanding from people who don[t understand evolution very well that there’s an “inherent assumption of progress/irreversibility.” A rat could evolve – not quite exactly into a snake, but it could get very long and thin and lose its limbs and maybe even someday evolve venom. It would be pretty unlikely to start laying eggs or become cold-blooded, I think, mostly because these are more integral changes and also a bigger advantage once you have them. Changing things like the reproductive system or the spine or the basic biochemistry of how the cell functions is harder than loosing legs or turning them into wings.

The spine evolved in a relatively simple little worm/slug. A blue whale could not just lose their spine and remain viable, and neither could most other vertebrates unless a lot of other changes happened first. Mammals couldn’t go back to laying fish-eggs because a lot of other changes have built up on top of how we bear live young – for example warm-bloodedness, young born too helpless to survive without nursing and parental care, expected nourishment through an umbilical cord attached to the parent’s blood and oxygen supply, and the time of development and quantity of nourishment required to develop a functional infant. You could fiddle with or reduce one or more of these characteristics, but yank too much of the foundation out and the building crumbles.

By comparison, gliding is pretty easy to evolve. Incremental steps can be taken that go from “unusually good at jumping/falling/landing through the rainforest” to “powered flight” without trying to change any of the “mess with this and you die or at least no offspring for you” that comes with changes to, say, the reproductive system.

On the topic of eyes, direct from Wikipedia:

Whether the eye evolved once or many times depends on the definition of an eye. All eyed animals share much of the genetic machinery for eye development. This suggests that the ancestor of eyed animals had some form of light-sensitive machinery – even if it was not a dedicated optical organ. However, even photoreceptor cells may have evolved more than once from molecularly similar chemoreceptor cells. Probably, photoreceptor cells existed long before the Cambrian explosion.[11] Higher-level similarities – such as the use of the protein crystallin in the independently derived cephalopod and vertebrate lenses[12] – reflect the co-option of a more fundamental protein to a new function within the eye.[13]
A shared trait common to all light-sensitive organs are opsins. Opsins belong to a family of photo-sensitive proteins and fall into nine groups, which already existed in the urbilaterian, the last common ancestor of all bilateral symmetrical animals.[14] Additionally, the genetic toolkit for positioning eyes is shared by all animals: The PAX6 gene controls where eyes develop in animals ranging from octopuses[15] to mice and fruit flies.[16][17][18] Such high-level genes are, by implication, much older than many of the structures that they control today; they must originally have served a different purpose, before they were co-opted for eye development.[13]

So basically, the eye certainly wasn’t starting from scratch when it evolved in different phyla. ‘Eyespots,’ simple light-sensitive protein clusters, were common in ancient single-celled organisms. Souping those primitive eyespots up can be done in many small individual steps, some of which may happen upon similar working formulas, without unduly troubling our friend Probability.

Same for echolocation. It seems weird to us because it’s a sense we barely possess, unless you count standing on a canyon yelling, or you’re Ben Underwood. But really what this tells us is that if you can hear and you can make noise, you can develop the ability to echolocate. It just takes more honing than sight does, so most of us don’t bother unless there’s some compelling reason not to rely on sight (blindness, hunting by night, hunting underwater in limited visibility).

What exactly do you mean by “construct of the mind?” If you mean that they are intangible and cerebral, well that’s fine: they’re in good company with most of the other ideas that humans hold forth.

But if you mean that they are based on imagination rather than solid data and math that anyone could follow, I recommend you actually look at the stuff you’re making such broad sweeping statements about at your earliest convenience. It’s not enough to say it’s all fiction; point out where the math is wrong.

“Cut off” is overstating, isn’t it? it just becomes hard to tell what’s one trunk and what’s a cluster of trunks all twined and grown into each other. It doesn’t kill the tree.

Note that the author is only arguing against the last of the three options. He is not in falsifying the first two, so if we are looking at the ToL as “a tracing of genomic and organismal history,” which I think is what we are concerned with, that’s still perfectly valid.

You might find this article of interest:

Established phylogenies at the level of primates are pretty solid. A vague speculation is nobody’s friend: do you think, say, the Old World/New World divisions of monkeys are spurious, or do you not think the genus Homo descended from the Australopiths?


(Ashwin S) #187

Pity you put the paper down… Shouldn’t it have been more trustworthy and hence worth a read?My observation is that the more a scientific paper conceptually agrees with creationist/ID ideas, the more it disses them.

I guess the purpose is to let everyone know the author is not an “IDiot” as many scientists like to call ID Scientists…

i suggest you read the paper and think independently… If my purpose was to quote-mine or misrepresent, i wouldn’t give links.
I have genuinely tries to show what the paper states.

Its internally inconsistent with the definition of evolution.Especially your view of God directing evolution.Your view is as much anti science as ID is… because its essentially the same as ID.
A sub class if you will.


(Ashwin S) #188

Perhaps it is.
We wont know until people have a look again at the genomes from a network perspective. It will happen at some point. We just have to be patient.
Till then, its just an opinion.


(Phil) #189

I think you are correct for some who espouse ID and some who promote EC. I think almost all who call themselves EC agree that life is intelligently designed, but that the best way to understand on a practical basis is science. However, the I D movement itself has its problems. Talk about a big tent. Even the FSM fits under it, in theory.


(Ashwin S) #190

Perhaps… But the way forward is not blindly accepting whatever is the consensus at a particular point of time. Its looking at the theological,philosophical and scientific merits of each case.
We should not be intimidated by accusations of stupidity, being anti-science etc.
Take common descent for example. I am sure you have heard debates on this. I will attach where the scientific debate is at.

Is this closer to what ID is saying or to what Talk origins is saying… we should not mistake scientific conservatism with science.

Edit: I really don’t get why someone like @gbrooks9 whose beliefs are far more similar to ID than anything to do with evolution should have such contempt for ID or YEC.


(Randy) #191

Sorry, what is FSM? Thanks


(Mervin Bitikofer) #192

Flying Spaghetti Monster I believe.

I had to think about it for a bit too, and I’ve been around the block on all these things more than a time or two. Pity any future linguists who without much helpful context come up against our current love affair with acronyms!


(Randy) #193

Thank you!IMHO U R right. :wink:
Medicine has a corny use of abbreviations too. http://gomerblog.com/2017/06/pgy1-writes-admission-note-that-does-not-contain-a-single-english-word/


(Mervin Bitikofer) #194

Kudos to you for refusing to be intimidated by name-calling, shaming, etc. It would seem we are agreed that science should be allowed to explore and speak for itself.

I read the article you linked at Sott.net. The title is catchy: “Why Darwin was wrong…” which I bet gets this article lots of hits. It starts off with a simple and true enough description of the tree concept. It goes on to suggest that the discovery of DNA, and then subsequent discoveries of how much HGT (Horizontal Gene Transfer) takes place have all made a big mess of the neat tree. The accuracy of their claims in that regard is best left to others here to evaluate. But what still caught my attention is that all the fuss addressed by this article seems to be confined to the eukaryotic / prokaryotic (i.e. ‘simple and early’) levels of life. But then I encountered this paragraph which speaks to my concern:

Hang on, you may be thinking. Microbes might be swapping genes left, right and centre, what does that matter? Surely the stuff we care about - animals and plants - can still be accurately represented by a tree, so what’s the problem?

Well, for a start, biology is the science of life, and to a first approximation life is unicellular. Microbes have been living on Earth for at least 3.8 billion years; multicellular organisms didn’t appear until about 630 million years ago. Even today bacteria, archaea and unicellular eukaryotes make up at least 90 per cent of all known species, and by sheer weight of numbers almost all of the living things on Earth are microbes. It would be perverse to claim that the evolution of life on Earth resembles a tree just because multicellular life evolved that way. “If there is a tree of life, it’s a small anomalous structure growing out of the web of life,” says John Dupré, a philosopher of biology at the University of Exeter, UK.

Okay – sure. If we go by linear time span, multi-cellular life is only a late-comer in the process and the bulk of life history on earth would only be observable under a microscope. And even today in terms of biomass, all the multicellular life, humans (and throw in all the animals!) are outweighed by the prokaryotes. Nothing new in any of that.

So my original simplistic concern about all this being relegated to one little singular “abiogenesis event” is given some proper perspective: it’s a billions of years long, messy, and (if the article is correct --which I’m provisionally open to accepting): little understood affair. So what? The “little bit” that interested Darwin and still captures much of our interest today is that branching out of life when it really started to get interesting. Isn’t most of the hoopla about the tree analogy (or bush or whatever people want to call it) forged from all the interesting stuff of the last few hundred millions of years?

So I read on to see if the authors would address this. Here is what they had to say (in their very next paragraph).

More fundamentally, recent research suggests that the evolution of animals and plants isn’t exactly tree-like either. “There are problems even in that little corner,” says Dupré. Having uprooted the tree of unicellular life, biologists are now taking their axes to the remaining branches.

Notice how the rhetoric changed here. Now instead of the rhetoric of "Darwin being wrong, or the whole tree being a mess or needing to be uprooted entirely; we hear instead: “There are problems …”. What? What happened to everything being a mess and not making any sense? Surely our rhetoricians aren’t falling down on the job here are they? Only a few problems? I was eager to see where they would go with this … and read on to see this paragraph.

Nobody is arguing - yet - that the tree concept has outlived its usefulness in animals and plants. While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another - a tree of 51 per cent, maybe. In that respect, Darwin’s vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him.

Did you miss that paragraph, Ashwin? This is from the article that you provided! It becomes apparent to me why you and so many others double down and focus so hard on the simple unicellular life (as dominant as it is in both time and mass). It is the only large canopy of refuge still available for those who want to hide behind problems and incomplete understandings. Not that they can’t also find many such remaining challenges in more recent evolutionary narratives too, but that picture is much more filled in (blurry as it still may be at some spots.) But the fact remains, if I see a photograph of the upper portion of a tree, I will recognize it for what it is regardless of the missing trunk that I can’t see because it’s not in my field of view. It could be a ten-thousand mile long trunk (or something else – not a trunk at all) for all I know. But what I do know is the bit of photo that is in view. And that’s the challenge you have to answer. It has problems – sure. But not near as many scientific problems as any competing narratives would create.

I’ll let the article have the last word in this conciliatory paragraph near the end of the article:

Even so, it is clear that the Darwinian tree is no longer an adequate description of how evolution in general works. “If you don’t have a tree of life, what does it mean for evolutionary biology?” asks Bapteste. “At first it’s very scary… but in the past couple of years people have begun to free their minds.” Both he and Doolittle are at pains to stress that downgrading the tree of life doesn’t mean that the theory of evolution is wrong - just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not. “We should relax a bit on this,” says Doolittle. “We understand evolution pretty well - it’s just that it is more complex than Darwin imagined. The tree isn’t the only pattern.”


The Appendix/Cave Fish Eyes/Etc. are (NOT) vestigial
(George Brooks) #195

@Ashwin_s, so, I have you on record stating that I.D. proponents advance an invalid form of Evolution?

You need to get off the fence, Ashwin. The one thing that BioLogos and ID has in common is God.

BioLogos, in its theological assertions, is quite different from I.D., in that it attaches a theological stance to the INCLUSION of mutation, natural selection, and speciation via common descent.

While a great many I.D. folks reject all three of these points in connection with the creation of new species.

Otherwise, BioLogos defends the right of scientists to not attempt to find God in science.

Ashwin, do you really have any idea what you are writing about? Or are you just here to attempt scoring points like it was a debating tournament?

[cc: @jpm, @pevaquark, @Mervin_Bitikofer ]


(George Brooks) #196

@Ashwin_s

I really don’t get why you don’t comprehend any of my explanations on this very issue.

  1. I accept/insist on God’s role in mutations (and its role in population genetics);
  2. I accept/insist on God’s role in driving Natural Selection in a teleogical manner;
  3. I accept/insist on God’s role in driving speciation by means of common descent - - ultimately from a single population of life on Earth - - ultimately requiring millions and millions of years for the currently extent species on Earth to arrive at their current state.

Do you know any I.D. supporters who share these three points with me? I would very much enjoy discussing additional topics with such a person. So… really … if you know an I.D. person that agrees with these 3 points, I need to meet them.

For example, based on recent discussions, neither @agauger or @RichardBuggs seem to share these positions with me.


#197

Oh really? When the paper starts with a statement that anti-evolutionists are mistaken in their interpretation of the author’s results that is a pretty clear sign that your interpretation, what every it is, is going to be wrong. You like to proof text with papers and it does get old after a while.


(Phil) #198

Merv is correct. I am guilty at times of intentionally throwing in a random reference just to broaden the thought process, and add a little humor, but that was a little obscure. Of course, referencing how ID originally did not state what or who the intelligent designer was (for legal/political reasons) so it could be space aliens or the deity(s) of choice.


(Mark D.) #199

But thinking independently is exactly what ID researchers do not do. All thinking is harnessed to the goal of reaching a pre-ordained result. How can anyone be said to “think independently” who does not engage in open ended inquiry?


#200

There is nothing in those papers that agrees with creationist/ID ideas. I have yet to find any ID/creationists who agree that ILS can create noise in phylogenetic analyses, and that all animals (from protists to humans) share a common ancestor and evolved from that common ancestor.

Do you or do you not accept the natural origin of rain clouds?


#201

Within that debate, there is full acceptance that eukaryotes share a common ancestor and that the tree of life for eukaryotes is real. Do you accept this finding?


(George Brooks) #202

@T_aquaticus

Perhaps you should word that question thusly?:

"@Ashwin_s, do you or do you not accept that God makes rain, in at least some cases, by natural lawful means?"


(Ashwin S) #203

First of all, i am glad someone actually article and manages a nuanced response. So kudos to you for that.
Yes, i did read that paragraph. And i agree with this statement :slight_smile:

Blockquote
Nobody is arguing - yet - that the tree concept has outlived its usefulness in animals and plants.

Blockquote
it is still the best way of explaining how multicellular organisms are related to one another - a tree of 51 per cent, maybe

The “yet” and “still” are significant and only time will tell which way the consensus will change.However, the author, even today is only willing to concede that 51% of the genetic material supports common ancestry…
And knowing biology, that % can go anywhere… up or down. (and its probable being contested very strongly)
So yes, for the time being, you will see it as a glass half full… and i will see it as half empty.
Only time will tell whether all the water will drain out of the TOL… I am patient in these matters.

Gunter Bechly… His belief is below.

Blockquote
Even though, intelligent design theory is in principle compatible with universal common descent and guided evolution, I personally have come to reject common ancestry as naturalistic mode of macroevolution in favor of a sophisticated version of progressive (Old Earth) special creation in terms of non-random adaptive macromutations in the “womb” of parental organisms (analogous to Schindewolf’s and Goldschmidt’s “hopeful monsters”, recently endorsed by Rieppel 2017, as well as other representatives of saltationism, mutationism and orthogenesis) combined with the instantiation of a new platonic form that preexisted as template in the mind of the designer (“special transformism” sensu Chaberek 2017). Nevertheless, I do affirm that every organism (apart from the first living cell) was produced / born from a biological parent organism and thus did not pop into being ex nihilo. I also affirm microevolutionary speciation within biological kinds through Neodarwinian processes. However, these never generate new specified complex information, but mostly represent devolution or variation or reshuffling of pre-existing information (e.g., homozygosity from heterozygosity, deactivation or detioration of genes, polyploidy, gene duplication, horizontal gene transfer, hybridogenesis). The two above mentioned affirmations may qualify as affirmation of universal common descent in the eyes of most evolutionary biologists, but the difference is that I only affirm common ancestry in terms of an unbroken lineage of individual maternal and paternal relationships (individual common ancestry), but reject the origin of new biological kinds from other biological kinds via transformation lineages of ancestral species (supraindividual common ancestry). The fact that because of the delicate and intricate interdependence of different genes and their products during ontogenesis, any transition necessarily has to include a coordinated major reprogramming of different genes as well as of epigenetic factors in the zygote cell, shows that the apparent distinction between guided evolution and special creation is rather blurry and in either case involves heavy physical intervention (coordinated and synchronized in multiple individuals within a population). When the distinctive genetic makeup is not inherited from the parents but introduced by design from an external intelligent agent, the process is rather akin to special creation than common ancestry.
Micheal Behe might also hold a similar position… Though i am not sure.

Thats is illogical nonsense for the simple reason that the author does not mention an specific. How can a general disclaimer falsify all conclusions made by a particular group? The only thing that makes sense is that he could be referring to the overall conclusion of “creationism”, or "“Intelligent design” and that he is against it.

I see it more as saving his backside.
Pls address actual content of the paper…


#204

So you expect us to believe an author that expresses “illogical nonsense”? Why trust the paper in the first place? I think you are trying to have your cake and eat it too.

He didn’t say that. Try to work on your reading comprehension. He just said his results can’t be used by anti-evolutionists.

And then you, an anti-evolutionist, want to use his results against evolution. Talk about illogical nonsense.

That may be your interpretation, but that is not what he said if you take a plain reading of the text.

Your opinion, but then again almost all of your arguments boil down to your opinion.