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

[Oneiric1975]

In Oxford, comma- omission is grounds for
divorce.

Hear, hear!

 

[SLP]

@Guy Threepwood wrote:

"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

I see you are back - how about some follow up?

 

[SLP]

@Guy Threepwood ran from this, as well:

@Guy Threepwood: "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

 

[Estrid]

@Guy Threepwood ran from this, as well:

@Guy Threepwood: "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

Now, don't be selfish.
If you deprive creationists of their
precious myths & junk what is left for them?

 

[FrumiousBandersnatch]

Cambrian explosion, among others

The more we learn about the period around the 'Cambrian explosion', the less like an explosion and the more like an extended period of multiple bursts of evolution it appears.

 

[Bradskii]

The more we learn about the period around the 'Cambrian explosion', the less like an explosion and the more like an extended period of multiple bursts of evolution it appears.

I think we can add that to Big Bang and Mitochondrial Eve as scientific terms that have confused so many people.

 

[FrumiousBandersnatch]

I think we can add that to Big Bang and Mitochondrial Eve as scientific terms that have confused so many people.

Part of the problem is that many who find evolution distasteful tend to cling to old evolutionary gaps & puzzles as indications of false dogma, without noticing that the gaps are progressively filled in and the puzzles become less puzzling as new data comes to light.

 

[Ophiolite]

I think we can add that to Big Bang and Mitochondrial Eve as scientific terms that have confused so many people

A cynic might suspect that a proportion of those people welcome confusion as a convenient excuse for facing reality. Of course, since I'm not a cynic, I'm confused as to how that thought entered my head.

 

[Gottservant]

Many creationists (and sadly, some biologists) seem to believe that 'macroevolution' is substantively different from 'microevolution.'

Short answer - it isn't, it is just many rounds of microevolution resulting in speciation.

So where is the selection pressure that would apply to other species? How would other species produce their version of human (or better)?

You have one equivalent of species to species relation, and you say "I can prove the justification of any species"? And the discovery you have made, just happens to be the same species as you?

Chance changes fortunes, but it doesn't favour those that make it a god.

 

[Bungle_Bear]

Chance changes fortunes, but it doesn't favour those that make it a god.

Yet that's exactly what your argument for God is.

 

[zoidar]

Nope. Dogs will always give rise to varieties of dog, and will never give rise to non-dogs. It would be a miracle if that ever happened.

Descendants will always be what they are descended from.

The ancestors of dogs may have been technically non-dogs, but naming something by what it isn't is silly, and you run into even sillier naming issues, wherein the 'non-dogs' give rise to dogs, which would technically make dogs a variety of 'non-dogs.' It's just a bad naming convention.

Better to call the ancestor of the dog what it is - a canine - and that makes things clearer. Canines gave rise to variety of canines, one variety is called dog. Dogs give rise to a variety of dogs, one of which is called poodle.

Not all dogs are poodles, but all poodles are dogs. Not all canines are dogs, but all dogs are canines. (All poodles are also canines).

I don't really get that. Then we are all fish, since we came from the ocean?

 

[Gottservant]

Yet that's exactly what your argument for God is.

The difference is parity.

I am quite happy to share the spoils of being a god, with my God.

You - on the other hand - would rather rule the Evolutionary roost, as though God couldn't do better.

 

[Bungle_Bear]

The difference is parity.

I am quite happy to share the spoils of being a god, with my God.

You - on the other hand - would rather rule the Evolutionary roost, as though God couldn't do better.

Please don't put words in my mouth or presume to know what I would rather. I pointed out that your argument for God amounts to nothing more than "I prefer my unevidenced claim to your well-evidenced claim" ie you're making chance (the possibility of a less likely explanation) your God.

Your arguments are facile, poorly thought through and often self contradictory. They display a complete lack of understanding of the science they purport to critique and really shouldn't see the light of day.

 

[Frank Robert]

So where is the selection pressure that would apply to other species?

It does, it is part of the process of evolution that makes them what they are.

How would other species produce their version of human (or better)?

They would need proper mutations, environment and selective pressures to do so. There were nine human species but only one had the population growth to out compete the others.

You have one equivalent of species to species relation, and you say "I can prove the justification of any species"? And the discovery you have made, just happens to be the same species as you?

[Chance changes fortunes, but it doesn't favour those that make it a god.

Evolution is not defined by chance alone and no one is claiming evolution is a god.

 

[Frank Robert]

The difference is parity.

I am quite happy to share the spoils of being a god, with my God.

You - on the other hand - would rather rule the Evolutionary roost, as though God couldn't do better.

There is parity. Theology is the study of god(s) and evolution is the study of a natural process. Evolution like all sciences are content being quite on gods and a good deal of theology is content with God created the natural processes.

 

[Ophiolite]

I don't really get that. Then we are all fish, since we came from the ocean?

Your Inner Fish: A Journey Into the 3.5 Billion Year History of the Human Body

 

[AV1611VET]

Your Inner Fish: A Journey Into the 3.5 Billion Year History of the Human Body]

Jonah's revenge?

 

[Phred]

Nope. Dogs will always give rise to varieties of dog, and will never give rise to non-dogs. It would be a miracle if that ever happened.

Descendants will always be what they are descended from.

The ancestors of dogs may have been technically non-dogs, but naming something by what it isn't is silly, and you run into even sillier naming issues, wherein the 'non-dogs' give rise to dogs, which would technically make dogs a variety of 'non-dogs.' It's just a bad naming convention.

Better to call the ancestor of the dog what it is - a canine - and that makes things clearer. Canines gave rise to variety of canines, one variety is called dog. Dogs give rise to a variety of dogs, one of which is called poodle.

Not all dogs are poodles, but all poodles are dogs. Not all canines are dogs, but all dogs are canines. (All poodles are also canines).

Otters are sea lions are seals are whales?

 

[Job 33:6]

I don't really get that. Then we are all fish, since we came from the ocean?

He's just saying that cladistics draw clearer lines than arbitrary words like "dog".

And yes, you're descended from fish.

 

[Subduction Zone]

I don't really get that. Then we are all fish, since we came from the ocean?

By cladistics we are fish. But to avoid breaking the fragile brains of deniers we say "We are vertebrates.". It says the same thing and is not quite as threatening.