For those wondering what "macroevolution" actually is...

[SLP]

Can you tell us the cause of these limitations? Once speciation occurs, there are no observable limitation to the further speciation of the resulting populations.

The hierarchical structure of any information system, including and especially digital ones like DNA

This forum software allows for adaptation yes?, you can tweak parameters for text size , shape and color. Just as we can tweak control genes for the size shape and color of dogs.
But you understand why you can never create a new feature, far less a new software application, by randomly tweaking the text parameters- it's not just a matter of how long you have, or how lucky you are- , the more definitive problem is that you are not accessing the proper part of the hierarchy.

Perhaps you can provide an example of a "new feature" that, say, a cow has that a platypus does NOT have, that is not a variant of an existing feature?

The hard wiring of the radio to constrain adaptation within a limited and viable range, is represented in DNA by the gene regulatory network- i.e. from this perspective adaptation is a design feature, not a design mechanism

From the perspective of those not in the biological sciences.

 

[SLP]

However I think cryptozoologists also have a good point when I ask for empirical evidence of Sasquatch: the north woods are mind mindbogglingly vast, & we have only searched a minuscule fraction of them.

Indeed - and some cryptic species have been "found" - the barking deer of Viet Nam, or even orangutans and gorillas, prior to their 'discovery' for example.

i.e. I'm not using the lack of direct evidence to dismiss the theory of evolution or Sasquatch, but like most people, I question whether the evidence is really as objectively 'overwhelming' as is often claimed by believers of each. If not direct observable evidence, what is it that strikes you as convincing?

Do you question that?
I have personally never seen a volcanic eruption, yet I accept that they have occurred in the past due to the sorts of evidence such events produce.

Regarding a lack of direct observable evidence, what convinces you of your Intelligent Design beliefs?
Allow me to constrain the possible responses - analogies are not evidence.

 

[SLP]

Here we go....

Darwinism had some very unfortunate 'real-world applications' according to many eugenics projects conducted worldwide over the last century , I certainly don't want to tar all, or even most believers in ToE with that brush.. but it has not all been positive

FFS...

And what about the Intelligent Design of war machines? Gosh - I'd hate to tar all Intelligent Designers with that brush, but, golly, all applications of ID have not been good.

See how stupid that "argument" is?

 

[SLP]

The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal

Cool - give it a try:

In vitro reconstitution of DNA replication initiated by genetic recombination: a T4 bacteriophage model for a type of DNA synthesis important for all cells

 

[SLP]

Correct me if I am wrong, but was it not Darwinists who long maintained that 'JUNK DNA' served no purpose, where skeptics long suspected it did?

You are wrong.
By 'skeptics', I think you mean creationists and Intelligent Design advocates.
Yes, they like to claim that they 'believed' all along that was no junk DNA - but not because of anything scientific. And they just claimed victory after-the-fact, without bothering to look at the scientific literature.

According to John West of the Discovery Institute, the first "prediction" that junk DNA would be functional was made in print by Bill Dembski in an essay from 1998, and had been implied in a rejected letter to the editor in Science penned by creationist electrician Forrest Mims in 1993.

Problem was, actual scientists had been speculating, predicting, and finding some function in some noncoding DNA a decade or more prior to the anti-evolution "skeptics" writing their little essays - just 2 examples:


Cell. 1975
Feb;4(2):107-11.
The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes.

By equilibrium competition experiments, the dissociation constant (K(RD)) of lac repressor for E. coli DNA carrying a deletion of the lac operon was measured at a variety of salt concentrations. These data are used in the consideration of several aspects of protein-DNA
interaction: Quantitative estimates of specificity are made. Specificity changes only slightly with salt concentration. We calculate that in vivo, 98 percent or more of repressor is bound to DNA predominately at sites other than the lac operator. Inducers shift repressor from operator to nonoperator DNA, but do not free it from DNA. The general affinity of repressor
for E. coli DNA is sufficient to support a model where repressor slides along DNA for significant distances. The effective dissociation constant of repressor for operator (K(eff)) is very sensitive to the total DNA concentration. We propose that "junk" DNA in eucaryotes functions to maintain total DNA at an optimum concentration. We consider the lac operon in the nucleus of a lymphocyte, point out that severe difficulties would be encountered, and suggest possible solutions.



Or Zuckerkandl from 1981:

A general function of noncoding polynucleotide sequences

Abstract

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a c-value paradox becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence motif that is variable within certain limits. Noncoding sequences of the chicken ovalbumin gene furnish an appropriate example of a sequence motif, GAAAATT. Its improbably high frequency and significant periodicity are
both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organism, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.


One can find an extensive list of citations and commentary on junk DNA here:
junk DNA « Genomicron

Of special interest are those tagged ENCODE:
ENCODE « Genomicron

A nice summary of 'junk' in the genome from biochemist Larry Moran:

Junk in Your Genome

Transposable Elements: (44% junk)

DNA transposons:
active (functional): <0.1%
defective (nonfunctional): 3%
retrotransposons:
active (functional): <0.1%
defective transposons
(full-length, nonfunctional): 8%
L1 LINES (fragments, nonfunctional): 16%
other LINES: 4%
SINES (small pseudogene fragments): 13%
co-opted transposons/fragments: <0.1% a
aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.Viruses (9% junk)

DNA viruses
active (functional): <0.1%
defective DNA viruses: ~1%
RNA viruses
active (functional): <0.1%
defective (nonfunctional): 8%
co-opted RNA viruses: <0.1% b
bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.Pseudogenes (1.2% junk)
(from protein-encoding genes): 1.2% junk
co-opted pseudogenes: <0.1% c
cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.Ribosomal RNA genes:
essential 0.22%
junk 0.19%

Other RNA encoding genes
tRNA genes: <0.1% (essential)
known small RNA genes: <0.1% (essential)
putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
transcribed region:
essential 1.8%
intron junk (not included above) 9.6% d
dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.Regulatory sequences:
essential 0.6%

Origins of DNA replication
<0.1% (essential) Scaffold attachment regions (SARS)
<0.1% (essential) Highly Repetitive DNA (1% junk)
α-satellite DNA (centromeres)
essential 2.0%
non-essential 1.0%%
telomeres
essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)
conserved 2% (essential)
non-conserved 26.3% (unknown but probably junk)

Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%
​

And from the same source, a nice review of Jon Wells - the fellow that took more than 10 years to earn his PhD, and had a whole 2 publications as a result - book on junk DNA. Part 1 (of several):
Sandwalk: The Myth of Junk DNA by Jonathan Wells

 

[SLP]

I think the evidence is pointing away from ToE in very much the same way as it pointed away from classical physics.

Darwinism came out of a Victorian age reductionist model of reality,

Ah, so you adhere to the common trope about how Darwin's theory is the same today as it was back then.

 

[SLP]

Agreed, and plenty new evidence keeps pouring in, not terribly favorable to Darwinism I would submit to you!

Would you submit that?

How is the evidence in favor of your preferred explanation coming along? Looks to me, based on what you've written so far, that there is still no evidence at all for creationsm/IDism and creationists/IDists are left today doing what they've been left having to do for the last several decades - attack evolution and make stuff up.

At the very least I find that tends to make for a more interesting discussion than trading accusations of dishonesty. That gets boring pretty quickly

Not as boring as the use of analogies as evidence; frequent unsupported assertion re: how 'the evidence' is not as supportive of evolution as it used to be, etc.; the use of quotes of dubious relevance; etc.

But if you have any substantive response to Raup's observation, I'd be interested in that

From RationalWiki:

Religious creationists are known for quote mining the work of Raup. Creationists usually quote mine Raup's paper titled Conflicts between Darwin and Paleontology (1979). The quote the creationists take out of context is:

“We now have a quarter of a million fossil species, but the situation hasn't changed much... We have even fewer examples of evolutionary transition than we had in Darwin's time."

What Raup really said in context was:

“”Well, we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn't changed much. The record of evolution is still surprisingly jerky and, ironically, we have even fewer examples of evolutionary transitions than we had in Darwin's time. By this I mean that some of the classic cases of darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information -- what appeared to be a nice simple progression when relatively few data were available now appear to be much more complex and much less gradualistic. So Darwin's problem has not been alleviated in the last 120 years and we still have a record which does show change but one that can hardly be looked upon as the most reasonable consequence of natural selection."​

The paper is a discussion about Darwin's mechanism of natural selection and whether this mechanism is reflected in pattern of the fossil record, not whether there is a lack of evidence for common descent. From the beginning of the article:

“”Part of our conventional wisdom about evolution is that the fossil record of past life is an important cornerstone of evolutionary theory. In some ways, this is true -- but the situation is much more complicated. I will explore here a few of the complex interrelationships between fossils and darwinian theory. . . Darwin's theory of natural selection has always been closely linked to evidence from fossils, and probably most people assume that fossils provide a very important part of the general argument that is made in favor of darwinian interpretations of the history of life. Unfortunately, this is not strictly true. We must distinguish between the fact of evolution -- defined as change in organisms over time -- and the explanation of this change. Darwin's contribution, through his theory of natural selection, was to suggest how the evolutionary change took place. The evidence we find in the geologic record is not nearly as compatible with darwinian natural selection as we would like it to be."​

 

[SLP]

I take your point, but I agree with Raup on this, there used to be more definitive examples of transitions between two distinct species, before they were thrown into doubt or discarded entirely

Something else Raup noted that has emerged in the record is the striking LACK of evolution in many populations- aka stasis

Horseshoe crabs for example have remained essentially unchanged for 100's of millions of years.

.. things show up in the record, remain virtually unchanged for long periods, then suddenly disappear/ are replaced with something else or are still here.. its very difficult to find good examples of beneficial gradual adaptation to any great degree

that was Raup's characterization of the record

that's not a verbatim quote but I'll see if I can find one, he made this point quite clearly in several instances- he was an early 'punctuated equilibriumist'

And Raup, as a paleontologist, looked only at morphology.

As one not constrained by a specialty, I am aware that while morphological changes are easier to see, non-morphological changes also occur. So why the expectation of solely morphological change?

 

[SLP]

I'm arguing that the disappearing transitionals are an example of conflicts between Darwin & Paleontology. That's exactly what Raup was talking about.

In 1979.

 

[Guy Threepwood]

This is all well and good from the purpose of explaining DNA at a conceptual level. But it doesn't mean that DNA and computer code are the same thing. They are not and never will be.

I do agree, of course on some level they are different.

But we are not at a complete loss- to make any inferences in science from our experiences of how we already understand the world to work - we chain the knowledge together, to figure out where each piece of the puzzle goes, to build a clearer picture of the unknown, right?

Sure superficial appearances can be deceptive, but if there's one reliable objective measure, it's mathematics- and that's what we are dealing with in digital algorithms.- whether running on a hardware platform of an abacus, silicon chips, or DNA

And again as Dawkins noted- the similarities to our own software design architecture, are not merely curious, they are uncanny.

There may be other evolutionary mechanisms at work, but such mechanisms would still fall under a theory of evolution. Keep in mind that like all theories in science, they are continuously updated as new mechanisms are discovered or existing mechanisms become better understood.

Agree again, and I think that's what we are seeing, the theory of evolution is turning emphatically away from Darwinism, it just gets semantically confusing since he kinda got dibs on the 'ToE' label!

It's refreshing to see someone using "Darwinism" in a non-derogatory manner here. So thank you for that.

Yes, it's really just to try to avoid confusion as above, if we define evolution as merely change over time, then we all agree with that, even Genesis!

This isn't about what a person "is". It's about what knowledge and scientific theories people apply to accomplish something. In the case of the theory of evolution, it has various real-world application as an application of the theory itself. Companies have even filed patents based on it for such applications.

Also, when I talk about functional identification and annotation of the genome I'm not necessarily speaking of junk DNA. I'm talking about the general search of the human genome to figure out what everything does. This is one of the research areas of modern genomics and something where the theory of evolution has been applied.

I can start digging up prior examples I've posted here over the years if you'd like.

Sure- you can give me just one for example if you like, I'm just saying that being skeptical of Darwinian evolution in no way precludes one from working in genomics, other than by possibly offending the vagaries of academic fashion that is.

 

[SLP]

to simplify:

The evidence is pointing more towards predetermination, information, instructions specifying how life develops - as opposed to a simple algorithm + random interaction.

Let us see some real examples of this evidence pointing to 'predetermination, information, instructions specifying how life develops.'
No essays, please - actual research demonstrating 'predetermination' in DNA.

 

[SLP]

Agree again, and I think that's what we are seeing, the theory of evolution is turning emphatically away from Darwinism, it just gets semantically confusing since he kinda got dibs on the 'ToE' label!

So, I guess you've never heard of the Modern Synthesis?
You really think that right up until.. today, I guess - evolutionary biologists are all strict "Darwinists" as in the original formulation of the ToE by Darwin as indicated in his 1859 book? Because that sure is what it looks like to me.

... I'm just saying that being skeptical of Darwinian evolution in no way precludes one from working in genomics, other than by possibly offending the vagaries of academic fashion that is.

I would add that this can also prescribe some rather dishonest activity on one's zeal to attack 'Darwinism' - look at the pathetic gaffes of Jeff Tomkins, creationist geneticist.

 

[SLP]

Because the gaps and jumps in the record were long held to be artifacts of incomplete data- punctuated equilibrium concedes to a large degree what skeptics said all along- the gaps are real, change does happen very suddenly, not gradually as predicted by the theory-

How much do you know about the relationship between genotype and phenotype/development?

And how about relying less on outdated quotes? THAT gets tiresome.

 

[SLP]

Overview
Scientific discussion meeting organised in partnership with the British Academy by Professor Denis Noble CBE FMedSci FRS, Professor Nancy Cartwright FBA, Professor Sir Patrick Bateson FRS, Professor John Dupré and Professor Kevin Laland.


The Royal Society, London
Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution

And yet, there were many evolutionary biologists at that meeting that not only disagreed with them but were able, on a couple of occasions to call their bluff.
It is all well and good to adjust theories as evidence requires - but from what I have read of these folks, they are more interested in leaving legacies.

 

[SLP]

Hello all- please excuse my jumping in here, but the skeptic's side seems a little under represented!

So do you accept that actual definition of macroevolution, and admit that creationists have been distorting and misrepresenting it due to either ignorance or malice?

Because that is sort of the topic.

 

[pitabread]

Sure- you can give me just one for example if you like, I'm just saying that being skeptical of Darwinian evolution in no way precludes one from working in genomics, other than by possibly offending the vagaries of academic fashion that is.

Again, I'd like to stress that an application of a scientific theory has nothing to do with what a person themselves believes. The application of the theory is independent of that.

As for examples, this paper on phylogenetics (the study of evolutionary relationships) lists a number of examples: https://cme.h-its.org/exelixis/pubs/CGP2005.pdf

The inference of phylogenies with computational methods has many important applications in medical and biological research, such as drug discovery and conservation biology. A result published by Korber et al. (19), that times the evolution of the HIV-1 virus, demonstrates that ML techniques can be effective in solving biological problems. Phylogenetic trees have already witnessed applications in numerous practical domains, such as in conservation biology (3) (illegal whale hunting), epidemiology (5) (predictive evolution), forensics (27) (dental practice HIV transmission), gene function prediction (7) and drug development (14). Other applications of phylogenies include multiple sequence alignment (11, 25), protein structure prediction (31), gene and protein function prediction (12, 22) and drug design (30). A paper by Bader et al. (2) addresses important industrial applications of phylogenetic trees, e.g. in the area of commercial drug discovery.​

 

[xianghua]

It will if you start simple enough.

but this is the problem- even the simplest eye is too complex and contain several parts. thus it cant evolve stepwise.

Also, if bacteria are (comparatively) simple and yet still have the largest population, it seems as if they're doing just fine. Not really any pressure on them to change, is there?

if so why complex animals evolved at all? they should stay as becteria too.

 

[Guy Threepwood]

but this is the problem- even the simplest eye is too complex and contain several parts. thus it cant evolve stepwise.

Yes, the eye has always been a good example of irreducible complexity, to the point where the necessary instructions are increasingly credited to pre-existing information- which is fine, but certainly not an example of Darwinian mechanisms at work..

 

[SLP]

Yes, the eye has always been a good example of irreducible complexity, to the point where the necessary instructions are increasingly credited to pre-existing information- which is fine, but certainly not an example of Darwinian mechanisms at work..

By information you mean DNA sequences.

Analogies are not evidence.

 

[Speedwell]

but this is the problem- even the simplest eye is too complex and contain several parts. thus it cant evolve stepwise.





if so why complex animals evolved at all? they should stay as becteria too.

You keep claiming that structures with several parts cannot evolve stepwise, but you never give any reason and ignore all explanation of how it can happen. What do you think? That if you continue to deny it, it will go away?