Sal's Flower?

And yet you claim that they’re “de novo”. You won’t say what you mean by that. Do you in fact mean anything?

How does it do that? You never say.

I predict that no creationist will attempt this. There is certainly no functional reason to expect a gene to be present in human and zebrafish but not mouse. This is just like asking how a raven is like a writing-desk, but different from a crow.

Look: you have no clue what any kinds are. Why not?


The way I am using the term means that they are unique to a group relative to the observed diagram. In this case Sal’s flower.

20 And God said, “Let the water teem with living creatures, and let birds fly above the earth across the vault of the sky.” 21 So God created the great creatures of the sea and every living thing with which the water teems and that moves about in it, according to their kinds, and every winged bird according to its kind.

It’s described as an original act of creation. From this we know that birds and fish are separate kinds.

Science is already working on this because of how well Zebra fish are optimized for discovery. I started looking at this in pubmed yesterday. Winston’s work fits very well with this research. Sal’s flower is a product of this research.

Because of the current state of molecular biology having a perfect set of trees representing kinds is not possible.

Yet the current state of molecular biology shows quite clearly that all living things belong to a single tree.

Are you counting on some future findings to show otherwise? Why should we expect this to exist anywhere other than your imagination?

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You quoted a bible verse and looked at pubmed yesterday.

This matter is now settled.


So you would agree that as far as you know all of them could have homologs in every species?

We only know that if a) you are interpreting the text correctly and b) the text is biologically accurate. How can you assume either of those things?

Sorry, dude, but the flower fits a tree. “Modules” that don’t fit the tree are a tiny part of the figure. The data don’t support a “dependency graph”.

That made no sense. You have no criteria for recognizing kinds even if you had perfect data, and you have no clue about what perfect data would be or would tell you.


They simply aren’t. You’re conflating the annotations with the genes themselves.

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I think we can infer from the data that this is not true. Winston’s graph of chickens, mice and zebra fish on page 14 show similar quantities of different genes. There are certainly annotation issues to be resolved.

These are basic assumptions we all make.

You are resorting to assertion and ignoring the magnitude of the problem for the tree of every module that does not fit. The repeatable mechanism that generates the pattern(reproduction) passes genes forward to their children.

Again, your resorting to assertion. The problem of clearly identified kinds can be improved over time by more clearly annotated gene families in the dependency graphs and better understanding of the functional dependence of genes. We can infer that chickens, humans, mice and zebra fish are separate kinds due to the gene differences in the dependency graph and their unique morphological features.

Winston’s graph doesn’t show genes at all. It shows “gene families”. At any rate, you miss the main point: that a gene present in species A but not in species B can still be homologous to another gene or non-gene sequence in species B. Orthology of genes is not the only common-descent relationship between sequences. Genes can be paralogous and they can be related to pseudogenes or other non-genes.

No, they aren’t. We make no such assumptions in science. They’re basic assumptions in creationism, but that’s quite a different thing.

The magnitude is small, since a tiny proportion of genes fall into those “modules”, small enough to be due to chance. With genes constantly being added and deleted, a few are bound to be deleted twice.

Yes, and every so often there’s a mutation that adds or deletes one. That’s what makes the pattern. If genes were just passed on without any changes there would be no pattern.

You can show me wrong by presenting your criteria.

How? You still haven’t managed to say. How are kinds identified?

That’s a start at a criterion. But how many differences and unique features are needed to make a separate kind? Are mice and squirrels separate kinds? Chickens and ducks? Zebrafish and goldfish? How would you tell?


Wikipedia has an example that might help clear this up for you, @colewd:

Paralogous genes are genes that are related via duplication events in the last common ancestor (LCA) of the species being compared. They result from the mutation of duplicated genes during separate speciation events. When descendants from the LCA share mutated homologs of the original duplicated genes then those genes are considered paralogs.[1]

As an example, in the LCA, one gene (gene A) may get duplicated to make a separate similar gene (gene B), those two genes will continue to get passed to subsequent generations. During speciation, one environment will favor a mutation in gene A (gene A1), producing a new species with genes A1 and B. Then in a separate speciation event, one environment will favor a mutation in gene B (gene B1) giving rise to a new species with genes A and B1. The descendants’ genes A1 and B1 are paralogous to each other because they are homologs that are related via a duplication event in the last common ancestor of the two species.[1]


Even better: suppose that one species loses gene B and the other loses gene A. Now we have one species with A1 only and another with B1 only. Still paralogous.


And, to make sure no one is missing the point, Sal and Bill would consider those to be unmatching or “de novo” genes between the two species. Am I right?

How are those coordinated mutations?


It’s not Sal and Bill that consider them that way. The figure ("Sal’s flower) does; it shows orthologous genes, and that’s all it’s intended to do.


OK, I see that now: Orthologue genes shared between the zebrafish, human, mouse and chicken genomes, using orthology relationships from Ensembl Compara 63. Genes shared across species are considered in terms of copies at the time of the split. For example, a gene that exists in one copy in zebrafish but has been duplicated in the human lineage will be counted as only one shared gene in the overlap.

That’s pretty clear.

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Where is the dependency graph with a list of specific genes, gene functions, and their distribution among species based on that function? So far, all you seem to be pointing to is noise in the phylogeny which is expected with common descent and evolution. On top of that, you have not even touched upon the possible presence of pseudogenes for missing genes. On top of all of that, even the authors of the paper where Sal got his flower mention the possible problems with the completeness of annotations:


That graph is not from the data. It is from annotations, which are incomplete interpretations.

Please stop misrepresenting them.

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I will point out that this entire discussion illustrates a wider problem with ID, where its proponents will take one small bit of information from the scientific literature, misunderstand it, then create a far-reaching argument from it.

The classic case is The Edge of Evolution, where Behe took a single offhand comment regarding a rough estimate of the frequency with which chloroquine resistance has emerged in malaria, and treated it as a firm and conclusive measure of the frequency with which any feature requiring two beneficial mutations can arise through evolution.


Please don’t ask Bill to make sense of his haphazardly chosen technical-sounding statements.


This is all possible but how do you move past speculation?

Your assertion is the separate patterns here are due to chance events. How do you show this really could be by chance given the allotted time between species/kinds?

The pattern could be a product of different trees. Do you think genetic recombination contributes to the pattern?

One additional criteria is if the two animal types in question can successfully reproduce. If they can that is an indication they are from the same kind.

By comparative genomics. For example, many candidate genes present in humans but not in chimps are commonly homologous to non-coding sequences in the chimp genome. Gene duplications can be seen if closely related species have one copy, while the studied species has two, one of them in the same location as the copy in other species. And so on.

I make no such assertion. But that’s a reasonable explanation. There are no “kinds”. But there’s a whole lot of time on those branches. The branch leading to chickens is around 300 million years long. Surely that’s enough time for a great many chance events.

No, it couldn’t. And no, I don’t, except that unequal crossing over can lead to new genes.

But what if they can’t? Does that tell you anything? And what is your argument that organisms from separate kinds shouldn’t be able to reproduce?