Kitzmiller, the Universe, and Everything

That’s like demanding data on planetary orbits independent of gravity assumptions. :slightly_smiling_face:


All of photosynthesis is non-controversial to those who buy into the dogma.
All of mitosis is non-controversial to those who buy into the dogma.

(It’s not a matter of “dogma.” It’s about evidence.)

Only one sperm out of many many millions manages to reach and fertilize an egg. So “successful” sperm are definitely rare among their peers. Nevertheless, there are 7.5 billion people on this planet. Rare events seem to happen a lot more often than never.

I agree 100%.

And if only there was some field of science whereby specially trained people investigated these better combinations and the changes in allele frequencies in populations over time. Maybe we could call it something like “evolutionary biology.” (On second thought, perhaps the simple name “biology” would be more than sufficient.)

Yes it is.


So are you really not going to read that paper because it wasn’t written by creationists?

Says it all.


Universal common descent by reproduction alone is dogma. Dogma that is used for thousands of papers. We do not have evidence of complex new structures arriving from reproduction alone.

In the same way plate tectonics is dogma and the germ theory of disease is dogma. You might want to look up the definition of “dogma” Bill since you seem to not understand the term.

If by “reproduction alone” you mean “empirically observed evolutionary processes” then yes Bill, we do have considerable evidence of that happening. Once again your ignorance of the evidence doesn’t make the evidence go away.


No you’re not, you’re basing the estimation of FI on comparative genetics. That’s how Gpuccio supposedly infers his “information jump”. So there you are, accepting a direction to historical genetic changes on the basis of a rooted phylogeny.

Do you remember that whole thing about having your cake and eating it too that I explained to you 10 days ago now?


Data are always independent of “evolutionary assumptions.” And the null hypothesis, in any phylogenetic analysis, is no discernible pattern of relationship between the taxa.

Now, if what you mean is that you would like to toss out phylogenetics entirely, you can do that. Two things, though:

First, you’re going to need an alternative hypothesis that explains the phylogenetic data equally well. The notion of fixity of species, coupled with the hypothesis that all species are sui generis, has not held up well under scrutiny, so you’re going to need something else. The only biologist in ID agrees that all organisms descend from a common ancestor, so you won’t get a lot of help from him – he may differ as to what conclusions he would DRAW from phylogenetics, but he certainly wouldn’t shut his eyes and say, “nah, nah, nah, I can’t hear this, this doesn’t exist!”

Second, unless you can show that this new species-as-sui-generis notion has some real explanatory power and a persuasive evidentiary foundation, you’re going to have one heck of a time selling it to anybody.


Yes, they are “rarely” observed on human life timescales. It was estimated that approximately 50 genes evolved pr. 1 million years in rice plants. That’s one gene every 20.000 years on average. No wonder we only see it rarely, nobody lives that long. We’ve only had the technolog to look for them for a few decades now.

But there are actual experiments where it has been shown that non-coding DNA can yield functional benefical protein coding genes. The papers on those have been linked, and you continue to completely ignore them.

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Are you talking about Joe Thorntons work?

No Bill, read the links given earlier. Here they are again:
Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW 2nd, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2020 Feb7;11(1):781. DOI: 10.1038/s41467-020-14500-z


Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast. Disruption of emerging sequences is generally inconsequential for fitness in the laboratory and in natural populations. Overexpression of emerging sequences, however, is enriched in adaptive fitness effects compared to overexpression of established genes. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich non-genic regions and subsequently accumulate changes molded by natural selection.

And this:
Knopp M, Gudmundsdottir JS, Nilsson T, König F, Warsi O, Rajer F, Ädelroth P, Andersson DI. De Novo Emergence of Peptides That Confer Antibiotic Resistance. mBio. 2019 Jun 4;10(3). pii: e00837-19. DOI: 10.1128/mBio.00837-19


The origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, and de novo from noncoding DNA sequences. Comparative genomics has generated strong evidence for de novo emergence of genes in various organisms, but experimental demonstration of this process has been limited to localized randomization in preexisting structural scaffolds. This bypasses the basic requirement of de novo gene emergence, i.e., lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them in Escherichia coli to identify short peptides that could confer a beneficial and selectable phenotype in vivo (in a living cell). Selections on antibiotic-containing agar plates resulted in the identification of three peptides that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic, and by inserting into the membrane, they reduce membrane potential, decrease aminoglycoside uptake, and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits and illustrates how expression of random sequences could spark the origination of new genes. In addition, our results also show that this question can be addressed experimentally by expression of highly diverse sequence libraries and subsequent selection for specific functions, such as resistance to toxic compounds, the ability to rescue auxotrophic/temperature-sensitive mutants, and growth on normally nonused carbon sources, allowing the exploration of many different phenotypes.

IMPORTANCE De novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel peptides in vivo using fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence pools in vivo and support the idea that expression of noncoding sequences could spark the origination of new genes.


But those aren’t by creationists, so they don’t count. Right, @colewd?


I find this remark really problematic. THIS initiated your interest in evolution? Not an interest in biology as such, but an interest in an objection to it which biologists don’t even regard as serious? Biology presents such wonderful things: an overview of the grand sweep of all living things; a deep dive into the intricate workings of living things; a beautiful and awe-inspiring vision in which even hagfish have a kind of glory about them. And none of that is interesting enough to spark an interest in evolution, but the idea that somebody thinks he’s rescued creationism from history’s dustbin by making an argument that things which routinely happen somehow do not happen at all is inspiring enough to get you started?

I know I say this a lot, but: there is NO POINT in taking in a critique of evolutionary theory unless you first understand evolutionary theory on its own terms. The critiques are deceptive; the portrayals of evolutionary theory contained in them are comically false in many cases. A critic who hopes to mount such a critique successfully must be a master of the field; and one who hopes to evaluate the critiques made by critics (most of whom are the very opposite of masters of the field) must be very, very careful to make sure he understands not only what the actual scientific consensus is, but WHY it is what it is, before he tries to take these sorts of things on board. STARTING with the critique is a sure way to reason yourself into a blind corner.

I have no idea what you mean by “reproduction alone.” If by this you mean reproduction without the generation of novelty, that’s not how living things work when viewed in large populations over long periods of time, so that’s sort of like saying that evolution without evolution is dogma.

Bear in mind that the notion of “complex new structures” as used by the IDCers is generally at the “cellular machine” level, in single-celled organisms – organisms with billions of years of history, and immense populations. How many “complex new structures” in this sense do you suppose it took to get a giraffe from a basal artiodactyl, or that basal artiodactyl from its 50-million-years-previous ancestors? Probably none. There is a tendency to assume that this claim that novel cellular “machines” are hard to make somehow translates to the domain of large eukaryote evolution. It doesn’t.


If true or not, it’s a great analogy.

My first goal was to find the accession number or the FASTA sequence of the minnow version of astrotactin 2.
To do that, I enter in the query box of the blastp page ( Protein BLAST: search protein databases using a protein query) the accession number of the human version of astrotactin 2 (O75129) and, in the “Organism” box of the “Choose Search Set”, I enter “minnow” and select several minnow species in the menu box. So doing, I get no result, presumably because the astrotactin 2 gene of the minnows species have not been sequenced yet. I then choose to blast human astrotactin 2 against the whole family to which the minnows belong, ie., Cyprinidae. To do that, I simply select “Cyprinidae” in the “Organism” box of the “Choose Search Set”. By doing so, the best match you get is with Carassius Auratus (CA), with a bitscore of 1807. I then use the accession number of CA (XP_026110708.) to perform the rest of the analysis.
As for what “Starfishes” is, here it is: Starfish - Wikipedia
Hope it help.

so take a look at this image. say that its an authentic image for the sake of the argument. will you conclude design?:

(image from wiki)

why not? see my image above. i think that the burdon of proof is on the side who claim that such a flying object doesnt need design. clear and simple.

It appears to me like there are some annotation problems with some of the protein sequences you have blasted. For example the piranha sequence (Pygocentrus nattereri) has a lower score compared to catfish and perch in part because only 60% of the query sequence you use from Carassius auratus is aligned to the piranha sequence. The gene-sequence is also listed as “partial”, and “COMPLETENESS: incomplete on the amino end.”

Another problem also seems to affect the highest scoring amphibian sequences which only have about 70% query coverage, as the sequence is only 925 amino acids in length, though is listed as “complete”. That result could be due to an actual ancestral deletion in the amphibian clade, incomplete sequencing, or a problem with the automated annotation process.

Even so, this is not that far off from what @Joe_Felsenstein said would happen. The most closely related fish to the Carassius auratus also show the highest blast scores, and bony fish(which mammals, birds, and lizards are more closely related to) in general score higher than do more distantly related organisms like cartilaginous fish. And that the scores gradually increase as align sequence from species more closely related.

And the further out you go, the lower the scores get. If you just blast against all of animalia but deliberately exclude vertebrates you can get a better picture of what exists “out there”.
I’m finding sequences in two different species of lancelet with about 80% coverage that score 345 and 278 respectively.
And a sequence in some parasite (Schistosoma japonicum) that scores 100. This indicates the protein we see in vertebrates evolved gradually from more distantly related ancestors, though it is certainly true that within the vertebrates the alignment scores are much better as they are much more similar in sequence within that clade. But as discussed before many times, that really just reflects conservation of adaptive positions against deleterious mutations.


I explained why not. Read my post again for that explanation.

What is that a picture of?

Do you also agree that the burden of proof is on those who do not believe was built and being piloted by intelligent beings who exist far outside our solar system?

If not, then you’re just making stuff up and not thinking your arguments thru very well.

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You do not look at that picture and say, “hey, a designed UFO”. You look at that picture and say either, “Wow, aliens from outer space!”, or you say, “Yeah right. Fail”. In other words, whether or not you see designed flying saucers depends precisely on whether or not you believe in aliens to begin with. You cannot split off the inherent issue of the identity of the designer from the perception of design. A preponderance of evidence might eventual alter one’s worldview, but that is so far lacking from the ID camp.

I’d conclude human design since that looks exactly like the human concept of a “flying saucer” seen in many 50’s Sci-Fi movies.

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