The definition and value of science

[The Barbarian]

That's not my point, especially when similar statements can be found in a number of textbooks. Here is another example of what I'm talking about.

Haeckel’s Embryos

Mostly, textbooks have the illustrations as cautionary stories about inferring things not in evidence. While is is true that Haeckel was right that embryos of tetrapods appear to have gill slits (actually branchial arches that give rise to gills in fish and jaws in other vertebrates) we do not become fish at some point in our evolutionary development. It's worth pointing out that embryology shows such tissues developing from common origins, without recapitulating all development. Creationists were outraged when textbook writers merely substituted photographs of the embryos which showed the same thing as Haeckel's drawings:

"Who you going to believe; me or those lying photographs?"

 

[The Barbarian]

I reject the Biology textbook portrayal of evolution.

Since it's directly observed all around us, and even most creationists have now conceded that speciation is a fact, there's really not much use in denying that it happens.

I suspect that you have confused evolution (change in allele frequencies in a population) or macroevolution (evolution of a new species) with a consequence of evolution (common descent). Is that the case?

 

[returnn23]

"... speciation is a fact..." Evolution is a fact? Not as described in Biology textbooks.

Evolution is fast except when it's slow.
Evolution makes a lot of changes except when it doesn't.

Take the coelacanth.

Living fossils: Liquidamber & Coelacanth

 

[The Barbarian]

The average person has no way of knowing when or if God intervened. I reject this as well.

Some IDers, like Michael Denton, agree with you. They think the "designer" set things up, got it running, and then walked away from it. Others like Michael Behe, accept the fact of evolution, but think God has to intervene periodically to get it to work the way He wants. They each have a part of the truth, but not all of it, IMO. Behe is a Catholic, BTW.

God upholds Creation moment by moment.

This is true.

 

[returnn23]

Intelligent Design is more than that. God did not make a wind-up toy called evolution, leave it on the ground and walk away. He did not let it go wherever it wanted. God intervenes continually.

Scientists Conclude: Human Origins Research Is a Big Mess | Evolution News

 

[The Barbarian]

"... speciation is a fact..." Evolution is a fact?

Directly observed.

Not as described in Biology textbooks.

I've reviewed a lot of biology textbooks. Almost all of them get it right.

Evolution is fast except when it's slow.

That was Darwin's prediction and it's been confirmed. A small population in a new environment will evolve quickly for reasons you could probably figure out. And Darwin noted that a well-fitted population in a constant environment would be prevented from evolving very much, by natural selection. And I think you could probably figure out why that is, as well. If it's hard for you, I could show you.

Evolution makes a lot of changes except when it doesn't.

Yep. For the same reason.

Take the coelacanth.

Interesting case. Ancient coelacanths were smaller, fresh-water fish. Today's evolved species (apparently 2 genera of them) are large, deep-water marine fish. Neither of todays genera are known in the fossil record.

Their closest living relatives are tetrapods and lungfish.

Genome Res. 2004 Dec; 14(12): 2397–2405.
Coelacanth genome sequence reveals the evolutionary history of vertebrate genes
Our results demonstrate that L. menadoensis is a vitally important species for understanding the evolution of tetrapod genomes, particularly in regard to the identification of tetrapod-specific genomic features. Using the protocadherin cluster as a measure of genome stability, it appears that coelacanth has little history or propensity for whole-genome duplication or frequent tandem gene duplications. Coelacanth protocadherin proteins have also accumulated fewer amino acid substitutions relative to their zebrafish and human orthologs. The modern coelacanth genome therefore provides access to the state of the sarcopterygian genome just prior to the emergence of tetrapods.

So why should coelacanths (and lungfish) be more closely related to us than to teleosts (like bass and catfish)? Because we and coelacanths share a common ancestor that lived after sarcopterygians diverged from the ancestors of teleosts.

 

[The Barbarian]

Intelligent Design is more than that. God did not make a wind-up toy called evolution, leave it on the ground and walk away. He did not let it go wherever it wanted. God intervenes continually.

There is a lot of disagreement among IDers on that. Some like Denton, are nearly deists. Others, like Behe, are more inclined to include God in the functioning of the Universe, only supposing He has to tinker with it because He can't make living things capable of evolving some parts. Some, like Johnson are pretty much YE creationists.

 

[returnn23]

"In The Edge of Evolution Michael Behe carefully assesses the evidence of what Darwin’s mechanism of random mutation and selection can achieve in well documented cases, and shows that even in those cases that maximize its power as a creative force it has only been able to generate very trivial examples of evolutionary change. Could such an apparently impotent and mindless force really have built the sophisticated molecular devices found throughout nature? The answer, he insists, is no. The only common-sense explanation is intelligent design.

"Michael Denton, M.D., Ph.D., author of Nature’s Destiny"

 

[The Barbarian]

Behe has only identified a few cases where he thinks God had to step in and fix evolution to make it work. And there, he's been contradicted by evidence. He mentions the prokaryotic flagellum. But it's been shown that most of it already exists in the Type III secretory apparatus:

Type III secretion systems: the bacterial flagellum and the injectisome
Type III secretion systems: the bacterial flagellum and the injectisome - PubMed

He's also argued that the blood clotting system is irreducibly complex and could not have evolved. But...

Cold Springs Harbor Symp Quant Biol 2009;74:35-40
Step-by-step evolution of vertebrate blood coagulation
The availability of whole-genome sequences for a variety of vertebrates is making it possible to reconstruct the step-by-step evolution of complex phenomena such as blood coagulation, an event that in mammals involves the interplay of more than two dozen genetically encoded factors. Gene inventories for different organisms are revealing when during vertebrate evolution certain factors first made their appearance in or, on occasion, disappeared from some lineages. The whole-genome sequence databases of two protochordates and seven nonmammalian vertebrates were examined in search of approximately 20 genes known to be associated with blood clotting in mammals. No genuine orthologs were found in the protochordate genomes (sea squirt and amphioxus). As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the "contact factor" proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans does not occur until pouched marsupials (opossum), at least one key factor still absent in egg-laying mammals such as platypus.

By definition then, the clotting mechanism cannot be irreducibly complex, since simpler functional versions exist.

Reality beats anyone's reasoning.

 

[returnn23]

Not so. The bacterial flagellum requires a number of things to happen together and work in a coordinated fashion. The question is, Where did the information come from to make the parts and where do the instructions come from to activate them? Upgrading from an allegedly primitive version does not solve the problem. I think you mischaracterize both Denton and Behe. I am sure those who think evolution does this would create stories that appear true, but that fail under close examination.

 

[The Barbarian]

Not so. The bacterial flagellum requires a number of things to happen together and work in a coordinated fashion.

Those things already exist in a simpler form in the Type III secretory apparatus. So it's pointless to say they couldn't.

Where did the information come from to make the parts

It's actually pretty interesting...

Uncovering the evolution of the bacterial flagellum
Uncovering the evolution of the bacterial flagellum | New Scientist

Evolution in (Brownian) space: a model for the origin of the bacterial flagellum
Abstract: The bacterial flagellum is a complex molecular system with multiple components required for functional motility. Such systems are sometimes proposed as puzzles for evolutionary theory on the assumption that selection would have no function to act on until all components are in place. Previous work (Thornhill and Ussery, 2000, A classification of possible routes of Darwinian evolution. J Theor Biol. 203 (2), 111-116) has outlined the general pathways by which Darwinian mechanisms can produce multi-component systems. However, published attempts to explain flagellar origins suffer from vagueness and are inconsistent with recent discoveries and the constraints imposed by Brownian motion. A new model is proposed based on two major arguments. First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria. Second, homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility. The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility. The selectability of each stage is documented using analogies with present-day systems. Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F1F0-ATP synthetase. (2) Much of the flagellum’s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization. (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events. (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components. Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum.
Evolution of the bacterial flagellum

I think you mischaracterize both Denton and Behe.

I'm just citing what they have said. But Behe seems to have reconsidered on at least one thing:

But the assumption that design unavoidably requires “interference” rests mostly on a lack of imagination. There’s no reason that the extended fine-tuning view I am presenting here necessarily requires active meddling with nature any more than the fine-tuning of theistic evolution does. One can think the universe is finely-tuned to any degree and still conceive that “the universe [originated] by a single creative act” and underwent “its natural development by laws implanted in it.” One simply has to envision that the agent who caused the universe was able to specify from the start not only laws, but much more.

[T]he designer took all necessary steps to ensure life. Those who worry about “interference” should relax. The purposeful design of life to any degree is easily compatible with the idea that, after its initiation, the universe unfolded exclusively by the intended playing out of natural laws. The purposeful design of life is also fully compatible with the idea of universal common descent, one important facet of Darwin’s theory.
Why I Believe in “Non-Miraculous” Intelligent Design | Dave Armstrong

He still doesn't think random variation and natural selection can do it all (he's vague on what else is needed) but this is a very large concession on his part.

 

[The Barbarian]

I am sure those who think evolution does this would create stories that appear true, but that fail under close examination.

I guess it would be useful for you to show us one thing that could not have evolved by variation and natural selection. What do you have?

 

[returnn23]

The problems with evolution are becoming more evident.

Swift

 

[The Barbarian]

The problems with evolution are becoming more evident.

Every scientific theory has problems to work on. If not, it's dead. They just aren't the ones you were told they were. You were going to show us one thing that could not have evolved. Have you found one, yet?

A quick look through journals will give you quite a number of things still under investigation.

But Darwin's basic points of evolutionary theory remain as solid as ever. If you doubt this, tell us one which has been refuted and show us how.

 

[returnn23]

You didn't look at the link I provided?

 

[The Barbarian]

You didn't look at the link I provided?

These things are not surprising in light of evolutionary development. Homeobox genes can utilize different embryonic cells to do the same things in different lines. But they are the same genes.

Development 2004 Feb 797-806
Hex homeobox gene-dependent tissue positioning is required for organogenesis of the ventral pancreas
In animal development, digestive tissues emerge from different positions of the endoderm as a result of patterning signals from overlying mesoderm. Although embryonic tissue movement during gastrulation generates an initial positional relationship between the endoderm and mesoderm, the role of subsequent endoderm movement against the mesoderm in patterning is unknown. At embryonic day 8.5 in the mouse, proliferation of cells at the leading edge of ventral-lateral endoderm, where the liver and ventral pancreas emerge, helps close off the foregut. During this time, the endoderm grows adjacent to and beyond the cardiogenic mesoderm, an inducer of the liver program and an inhibitor of the pancreas program. The homeobox gene Hex is expressed in this endoderm cell domain and in the liver and ventral pancreas buds, after organogenesis. We have found that in Hex(-/-) embryos, there is a complete failure in ventral pancreatic specification, while the liver program is still induced. However, when Hex-null ventral endoderm is isolated prior to its interaction with cardiogenic mesoderm and is cultured in vitro, it activates early pancreas genes. We found that Hex controls the proliferation rate, and thus the positioning, of the leading edge of endoderm cells that grow beyond the cardiogenic mesoderm, during gut tube closure. Thus, Hex-controlled positioning of endoderm cells beyond cardiogenic mesoderm dictates ventral pancreas specification. Other endodermal transcription factors may also function morphogenetically rather than by directly regulating tissue-specific programs.

You were going to tell us which of Darwin's basic points of evolutionary theory have been refuted. What do you have?

 

[returnn23]

I no longer believe in common descent based on the conclusion reached from the article I linked to. Whatever happened, it is inconsistent with common descent.

"It is more than 20 years since Raff wrote: “One might reasonably expect mechanisms of early development to be especially resistant to modification because all subsequent development
derives from early processes” [3], and the more we find out about
how embryonic development is implemented at the genetic
and molecular levels, the more it reinforces this commonsense
conclusion. Many other authors have also commented on why
we would expect early embryonic development to be resistant
to change (for examples see Irie and Kuratani [7]). Yet, when
it comes to the diverse embryonic development of presumed
homologous organs or body-plans, the usual assumption is that
their early development must somehow have derived from that
of a common ancestor, no matter how improbable the changes
required, rather than accept the plain inference that the similar
organs etc. are not homologous, at least not in an evolutionary
sense.12 This expectation seems to reflect an ideological com-
mitment to the theory of evolution rather than an objective
assessment of the embryological facts."

 

[The Barbarian]

"It is more than 20 years since Raff wrote: “One might reasonably expect mechanisms of early development to be especially resistant to modification because all subsequent development
derives from early processes”

That was apparently written about 11 years ago, and refers to a time before the science of evolutionary development made it clear that homeobox genes could use cells of different origins to produce bodies. No link was given, but this one fell by the wayside a long time ago.

For example your guys were assuming that Haeckel's idea of recapitulation is valid. But as you learned, branchial arches (for example) form gill arches in fish and jaws and other structures in tetrapods.

Yet, when
it comes to the diverse embryonic development of presumed
homologous organs or body-plans, the usual assumption is that
their early development must somehow have derived from that
of a common ancestor,

Homeobox genes do verify that. Would you like to learn more about it?

Evolution of homeobox genes
Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks.
Evolution of homeobox genes - PubMed

This is not news. The abstract is from a journal article a decade old.

Linnaeus first found evidence of common descent in the 1700s. When it became possible to test Darwin's inference of common descent by genetic analysis, the data showed it to be true. Phylogenies based on DNA clearly show common descent. And we know it works, because we can test it on organisms of known descent.

 

[returnn23]

All ideas related to common descent are questionable. This is not the first time I've brought these issues up. "a decade old" article does not matter as long as the findings are accurate. I've read other journal articles and too many assumptions are included like "must have," "likely led to" and similar. I think researchers who were told evolution is true add a bias to their work.

Why Do We Invoke Darwin?

 

[The Barbarian]

All ideas related to common descent are questionable.

Everything in science is to be questioned. That's how theories are formed and become more robust over time. Or they fall.

All ideas related to common descent are questionable. This is not the first time I've brought these issues up. "a decade old" article does not matter as long as the findings are accurate.

It's just been found to be incorrect, based on genetic and embryological data. The science of Evolutionary Development has come a long way in those decades.