Gene Tree Incongruence

Of course I’m serious. Unless someone else is writing your posts for you, who do you suggest I blame for your lack of a model?

2 Likes

I try to avoid commenting on subjects I don’t know anything about. I don’t know anything substantive about evolution of transcription factor binding sites.

Can any of you clever folks cite the BioLogos narrative which requires that life had to emerge from dead chemicals without God’s assistance?

This requirement does not exist.

1 Like

This usually occurs with a range of well known processes. Just one mechanism is transposon hopping, which often carries TF binding sites. But given how short TF binding sites are, it is even possible for some to arise by cumulative point mutations. The cool thing about these mechanisms is that it enables “analog” adjustments to gene expression, which are usually well tolerated and usually introduces “safe” variation into the population that can later be selected.

Of course this is well known. Ignorance of the well known is not a good argument.

Maybe @praveens can add to this, because this is actually his area of research.

1 Like

It would be well for BioLogos critics to remember this !

1 Like

Let me clarify this for you. There are many different kinds of problems with common descent. It fails in every way imaginable. For example, convergence is rampant in biology. Highly complex, detailed designs are repeated in distant species. The cephalopod and mammalian vision systems are remarkably similar in incredibly detailed ways. There are differences but, according to evolution, the detailed repeated designs must have arisen independently. Instead of common descent, you have to have independent random mutations creating the same detailed, complex, designs. All this for completely different kinds of organisms, in completely different environment, in completely different parts of the world. The data do not fit the common descent model. There are many, many, many more examples where those came from.

Then there are divergences, incredibly different structures in allied species. Like convergence, divergence is rampant in biology.

Then there are incongruent characters, which produce significantly different phylogenies. Then there are missing and isolated characters where phylogenetic comparisons are not even possible because a character does not even exist in the neighboring species, or is lineage-species, etc.

The data do not fit the common descent model.

For the two microRNA articles I linked, the first one, contrary to your rosy reading, is an example of rampant incongruence—not merely in “precisely the places where the signal is most difficult to make out already.” As Pisani explained in the article: “What we know at this stage is that we do have a very serious incongruence.” And as Peterson explained: “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree.”

So for the n-th time, evolutionists are busy constructing new epicycles to patch up the problems.

The data do not fit the common descent model.

I love clarity. And here we have it. I gave the evolutionist a fair chance to back away from this. Common descent is a fact because … why? Because the world isn’t random. His common descent model is failing at every turn, but not to worry, it must be a fact because the species aren’t … what? Aren’t random.

Unbelievable.

The myriad failures and contradictions literally do not matter. We are now getting a look at what this is all about.

Well let me help you out.

TF binding sites massively contradict common descent. There is no correspondence. You could read this paper which unexpectedly finds that transcription factor binding is not conserved between mice and men: “we found that the binding profiles of OCT4 and NANOG are markedly different, with only approximately 5% of the regions being homologously occupied.”

Or you could read this commentary on those findings, which explains that:

But it gets worse:

And, as the authors explain, there are more such “lineage-specific” findings, where those came from:

Of course there have been no observations of “network rewiring,” lineage-specific or otherwise. This is yet another unfortunate misrepresentation of science. What has been found is that the data contradict common descent.

@Cornelius_Hunter

So what do all your conclusions amount to if Geology proves that the Earth is billions of years old?

But only in the most stereotypically pseudoscientific way. At no point do you actually engage on the evidence.

You have neither mentioned nor discussed a single datum, so I have to doubt your alleged finding.

@Cornelius_Hunter

You are deciding how to interpret Genesis based on This?!:

"You could read this paper which unexpectedly finds that transcription factor binding is not conserved between mice and men: “we found that the binding profiles of OCT4 and NANOG are markedly different, with only approximately 5% of the regions being homologously occupied.”

You need to come up for air!

I’m not sure how Genesis got into this. I’ve been talking about the science.

@Cornelius_Hunter… but to what end?

Aren’t you trying to prove that Evolution without God can’t happen?

So… here in BioLogos … we think God is involved. Lots of different opinions about HOW God is involved… but I think God has worked out the bugs in that molecular issue you are describing, right?

So that means you and I are on the same team, yes?

George

Well evolutionists talk a lot about theology. I used to be an atheist and I was an evolutionist. Then I was saved and became a Christian. I remained an evolutionist as I had no reason to doubt it. But then I got interested in evolution on a lark–I happened to hear what evolutionists were saying about it, and the claims they were making seemed strange. I wasn’t against evolution, but rather was neutral. It was OK with me if it was true, but it was also OK with me if it was false. I didn’t have any baggage on the topic. I found that many evolutionists do have baggage on the topic. There is a lot of religious talk, and evolution must be true for non scientific reasons.

Because, for me, it was OK if evolution was false, I was free to explore the science objectively. As a scientific theory, evolution is terrible. It lacks explanatory mechanisms, its fundamental predictions are all falsified, it is incredibly complicated, and it is religiously motivated. Evolutionary thought has a long history that goes way back. You could resurrect arguments from two millennia ago, between the Epicureans and Stoics, and they literally would fit right into today’s discourse. People have sought naturalistic origins for thousands of years, probably for as long as there have been people. There is nothing new in modern evolutionary thought. The idea that the world, especially the biological world with its millions of species, evolved is simply not scientific.

So… Let me get this straight. Do you mean to imply that almost all members of the scientific community worldwide (including loads and loads of Christians) are involved in some sort of religiously naturalistic conspiracy? And you are the “objective” observer engaging in “true” science to debunk the myth?

If that’s your conviction, there’s not much to be gained from this conversation. In the Netherlands we would say you’ve been hit by a windmill.

[credit: Stuff Dutch People Like]

3 Likes

This is an uncharitable response as there are many scientists who have serious doubts about ToE as it is promulgated these days. I am a scientist, and on the rare occasion when we waste our time discussing ToE, we scientists express opinions that are not dissimilar to those given by @Cornelius_Hunter. It is not to say that we think of a conspiracy, but rather the primitive and inadequate theory that makes such extravagant claims re scientific verification, and the obvious (some may say blindingly obvious) ideological baggage that has always accompanied this inadequate paradigm of biologists.

I have no problems with expressions of criticism of evolutionary theory (or some popular versions of it), purely based on its claims or assumptions.

The craziness problem starts when it is insinuated (as Cornelius does) that the scientists who accept common descent are doing so purely (or primarily) because they are driven by a certain ideological agenda. Now that’s uncharitable towards the thousands of biologists (with very diverse belief systems) who have devoted their lives to this field of scientific inquiry. It is also an unjust accusation of many of our fellow brothers and sisters in Christ who are biologists.

2 Likes

Perhaps I should read all of the comments to see what may have been insinuated - my response is directed to the notion (or implied assumption) that all scientists accept the ToE as it stands, and thus anyone else must be odd or whatever. The comments I have read leave me with the impression that Cornelius has done a lot of work and developed his outlook with effort and interest. I would add that the range of opinions offered to ToE (be it as support or as criticism) points to an (obvious to me at least) failing if taken as an established paradigm.

It does lead to a great deal of discussion and debate - which I think is part of the wider interest in biology as the science that deals with life on our planet.

Hi George. There’s only one comment you would need to read. My response was triggered by the most recent message of Cornelius. I’ll highlight some quotes for you:

These are just a few examples of unjust insinuations made towards those who work within the evolutionary paradigm. Unfortunately, such assertions are very common in young-earth / intelligent design circles. My intention was to point out that the implications of such claims are just too extreme to be even slightly tenable (e.g., it would imply some kind of worldwide ideological conspiracy with cooperation from many Christians).

That’s a non sequitur. For example, we’re also still having lots of discussions on the age of the earth among Christians, but that does not mean that the old-universe / old-earth paradigm is failing in any way. The big picture is there already, the details are under revision. Most of the friction seems to be due to certain theological and exegetical “paradigms” that are being thwarted by the increasingly well-established science of common descent and the old age of the earth.