Evolution: the Facts.

[Kotatsu]

You veer off when saying "they are the expressions of the same preserved genes." He does not say that. Could be. But that's adding a little bit of your paradigm and making an assumption.

My apologies. They would be developments by a mechanism Davison calls "a complete mystery" of the same information which has been carried in these (and all other lineages) since time immemorial in unspecified information carriers.

Btw, are they expressions of the same preserved genes?

Why do you ask someone whose understanding of these matters is so demonstrably inferior to your own?

Meanwhile, could you explain what purpose the following extract from Davison's paper serves, from a purely scientific point of view (emphasis as in original):

"The very word evolution derives from the Latin evolvo meaning to unfold as the pages of a book. Needless to say, a book has, by definition, already been written."

I find it highly curious that a professor in biology has never seen a notebook.

Why would they have to?

Because they have different functions.

Based only on "Ontogeny...", we know that Davison is interested exclusively in function. Structure, development, homology -- these are all concepts that Davison has either not heard about, don't understand, or don't care about. Sure, there are references to both developmental characters (both "higher" insects and nemerteans are said to have imaginal discs) and structure (e.g., the eggs of vertebrates), but no attempt is made to show that these comparisons are relevant.

If I were to write a paper criticizing evolutionary theory, I would expand on what evolutionary theory says about these perceived similarities, how evolutionary theory explains them, cite the evidence that this interpretation of the natural world is wrong, and propose a more solid hypothesis to explain the same phenomenon. This would be the more rudimentary form of scientific critique that I would expect to be taken seriously by other scientists.

By contrast, Davison mentions that two taxa -- or "kinds" really -- have a feature in common that he believes is the same thing, because they share the same function. He then proceeds to the next example, and the next, and the next, which would be acceptable, if at the end there would be some exploration of the evolutionary hypotheses for these patterns, some data that falsifies these hypotheses, and a proposal for a more robust hypothesis that would explain them.

We don't get that from Davison. Once he is finished listing his examples, he dives directly into arguments from personal incredulity -- "Rather than assuming independent invention of these remarkable parallels, it seems to me more reasonable to postulate these events resulted from the activation (derepression) of an enormous yet clealry limited stockpile of potentialities which were available when those events took place." and so on -- and then a page-long appeal to perhaps consider God, because a lot of people we connect with intelligence mentioned God in their work at some point.

Well, there is also the charming statement that "How such transformations were effected remains, of course, a complete mystery", meaning that even having gone through all these examples and -- hopefully -- having read, but not cited, all the relevant literature, Davison still has no clue about how his own mechanism is supposed to work, but as "macroevolution seems no longer to be in progress, we may never be able to resolve that issue."

So we know that to Davison, function is the only thing that matters, regardless of structure. Same function = same information that is preformed. Does the animal you're studying have a "kind of placenta"? Then it "exhibits characters of [...] placental animals". Structure, development, homology, and other factors never come into the picture.

Since similar functions are evidence for the information being preformed, and all organisms contain all the information required to develop any organism, then I believe it follows that there is an implied need for separation between the preformed information needed for the function of a wing and that needed for the function of a fin, as there are plenty of organisms that have one but not the other. Otherwise, developing the information for a finwing into either a fin or a wing would lead to these being randomly developed in any given population of birds or fish.

Of course, the same preformed information could result in a wing or a fin depending on reliance of the completely mysterious mechanism that is supposed to derepress these potentialities in the first place. Like many smart people throughout pre-genetic history, we could for instance consider God.

You are oversimplifying Davison's claims

This is impossible. His claims are already so childishly simple that nothing that contains difficult words like "gene" or "homology" could possibly be a simplification.

Prove it. That's not what standard evo theory says, at least not right after the isolation. Dinwar showed no such thing.

I will certainly try, and hope that someone else will be able to correct me if I am wrong.

Let us assume that we have a population of size X, which is genetically identical except for Y individuals that each have a genome that is different from that of the non-Y individuals, and also from each other, so that no member in Y has the same genome. Let us assume that Y is randomly distributed in the population. We can simplify the diversity (D) as:

D = (Y1 + Y2 + Y3 + Y4 + ... + Yn + 1)/X = (#Y+1)/X

A change occurs, and a random subsample is isolated from X. We call this subsample X', and put a ' on all members of Y that are randomly included in the isolated population. The diversity for this isolated population can be simplified as:

D' = (Y'1 + Y'2 + Y'3 + Y'4 + ... Y'n + 1)/X' = (#Y'+1)/X'

X' is by definition always smaller than X, as it is an isolated subset of it. Y', however, being a randomly selected subsample of Y, may be equal to (if all of Y is in the isolated X') or smaller than (if only some Y are isolated) Y.

It follows that D' = D (the genetic variation is identical) if for instance:

(#Y'+1)/X' = (#Y+1)/X

That D' < D (the genetic variation is lower) if:

(#Y'+1)/X' < (#Y+1)/X

And that D' > D (the genetic variation is higher) if:

(#Y'+1)/X' > (#Y+1)/X

That is, if the proportion of Y' to X' is higher than the proportion of Y to X was, genetic variation has increased in the isolated subpopulation. If X = 100 and Y=25, this means that every fourth individual in X has a unique genetic sequence. A random subsample of X' = 10 where, by chance, we get Y' = 5 means that every second individual has a unique genetic sequence, which means that the variation of X' -- measured in this clumsy way -- has doubled. In the extreme case of belonging to Y meaning that you are more likely to end up in Y', we could have a population X' = 10 which contains only Y' individuals, in which case the genetic variation that is 100%, as opposed to the initial 25%.

This primitive model ignores, of course, phylogenetic relatedness within Y and between Y and X, geographical substructuring of X prior to isolation, and the effect on the lineage's survivability of Y and X, respectively.

 

[Kotatsu]

In order for you to make that claim, you'd have to actually understand what evolutionary theory is and as such, it's a fallacious statement.

Not at all. All ST needs to know to be able to disprove your claims 1 and 4 would be some basic knowledge of taxonomy. By definition, no recent population can evolve into a previous taxon, because this reversed taxon would not share an exclusive common evolutionary history with the type of the more ancient taxon. It is as simple as that, really.

This statement can be based entirely on the way you have formulated your claim in combination with a knowledge of basic taxonomy. No further information about evolutionary theory is required.

I hope Randman's obstinacy won't discourage you fromcontinuing to post. Perhaps your interventions won't sway Randman's opinions, nevertheless they are valuable to me and probably to others. To illustrate:

In post 1071 I wondered how the presence in epidinium of ''esophagus'', ''skeleton'', ''rectum'', and ''nervous system'' could relate to those same ''organs'' in multicellular organisms. Now it is clear that those structures are analogous but not homologous. The genetic information for their structure is entirely different. Those organs did not develope in multicellular organisms because the genetic information was preformed in protozoan genome, but rather a different DNA pathway was developed.

Yes, I saw your post, but didn't have time to answer it as I was writing my review of Davison's idiocy at the same time. Glad that you got your answer anyway!

But I never said it was definitive proof against evolution but merely indicative of how evos rely on overstating things, claiming they are facts when they are not, and making wildly premature, dogmatic arguments not based in a careful examination of what we do know from the data and do not.

I think this is the most rewarding aspect of your posts, randman. Almost every time you make a statement about how you perceive "evos", we need only look into Davison's "Ontogeny..." and find the exact same thing there, typeset by the man who made the Hollywood sign.

"Evos" overstate things? Well, Davison claims that structures with similar functions in distantly related organisms is clear evidence that they have preformed information that is derepressed by a completely mysterious mechanism we may never know about, but we can be dead sure that this is the case, because Peripatus has "a kind of placenta".

"Evos" claim things are facts when they are not? Well, Davison claims that macroevolution has stopped and that there are no intermediates in either the fossil record or among extant taxa.

"Evos" make premature statements without considering the data? Well... I think the whole word "analogy" sums up what Davison does that is comparable. The fact that he has chosen to deliberately ignore all scientific literature after 1973 is also an indication that he is not very keen on considering all the available data before making his conclusions.

And the fun never stops. Again and again, you claim that something is a necessary consequence of evolutionary theory without backing it up with more than pure assertion. After having explained why the patterns you claim should be everywhere if evolutionary theory is correct are not in any way predicted by evolutionary theory, I find that these patterns are necessary consequences of Davison's hysterical theory.

Your concept of reversibility, for instance, is certainly possible, but extremely unlikely even over just a few generations according to evolutionary theory, so we wouldn't expect to find this pattern at all if evolutionary theory is correct. However, if Davison is correct, this should happen everywhere, as all organisms already contain all the information to produce any other organism.

I am actually starting to look forward to reading Davison's other articles, so I will just leave your discussion about horses behind, as I still haven't had time to look at it, and this promises so much more comedy value. However, if you want to give the appearance of intellectual honesty, randman, you would do well to just ditch Davison and pick up some other creationist to base your arguments on, because Davison is a failure even as a creationist, and that is not something to be inspired by.

 

[Squeegee Beckenheim]

However, if you want to give the appearance of intellectual honesty, randman, you would do well to just ditch Davison and pick up some other creationist to base your arguments on, because Davison is a failure even as a creationist, and that is not something to be inspired by.

I think he's probably too invested in his position to do that. It's true that the more you read of Davison the more you see where randman is coming from, as he's basically just parroting it all back.

In one of the other threads he made the argument that a mouse and a marsupial mouse were identical, and maintained this position even when it was pointed out to him that the only thing they had in common was a similar appearance. That's a different example, but is straight out of Davison.

 

[ThunderChunky]

This primitive model ignores, of course, phylogenetic relatedness within Y and between Y and X, geographical substructuring of X prior to isolation, and the effect on the lineage's survivability of Y and X, respectively.

The subpopulation still has less total genetic variation in your example. It just has more variation per individual.

 

[Kotatsu]

The subpopulation still has less total genetic variation in your example. It just has more variation per individual.

But that is exactly what I was asked to prove (emphasis added):

A subgroup that is isolated from the mother population may have higher relative genetic variation than the mother population, it may have lower relative genetic variation, or it may have exactly the same relative genetic variation.

 

[Paulhoff]

The problem is in-breeding does not increase fitness in the long run as you guys claim.

Evolution has nothing to do with in-breedging.

Paul

 

[Dinwar]

However, if you want to give the appearance of intellectual honesty, randman, you would do well to just ditch Davison and pick up some other creationist to base your arguments on, because Davison is a failure even as a creationist, and that is not something to be inspired by.

randman gave up all pretense at intellectual honesty when he began refusing to read posts merely because the post's author disagreed with him. He further abandoned any claim to honesty when ANTpogo demonstrated conclusively that his statement that "evos" use Hekel's flawed embryology work was completely wrong (including a reference to the paper randman used as support for HIS possition--a common theme in these three threads). I say this not as an ad homonym attack against randman--he's doing well enough on that front without my help--but rather to point out that he's not interested in honest debate, nor is he interested in learning anything, and therefore this argument is going to be meaningless to him.

 

[randman]

No, it is not. It is not predicted to be as genetically complex as worms, insects, or vertebrates. It is now predicted to have some genes that it was previously predicted not to have. This is because the previous prediction was based off very few data points, it was not some limit of expected complexity, it was just based off of the data that was available. We now have a new data point, so the predictions are revised.







Like I have told you numerous times, the studies do not indicate LCA was "so genetically complex." You are reading the studies without understanding them, you probably need more education.



You really do not know what you are saying. The one paper you cited has nothing to do with plants. Plants diverged from the animal lineage long before animals themselves diverged.

Few points. I am not just reading one paper. Look into the matter and you will see what I am saying is true. The LCA of animals is not just predicted to be more genetically complex than worms, and the LCA of plants and animals is thought now to have "more types of genes available" to them than plants and animals have today.

Note this comment (different studies).

"The cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals," explains William Loomis, a professor of biology at UCSD

http://www.biology-online.org/articles/biologists_determine_genetic_blueprint.html

 

[Dinwar]

Full quote:

"The cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals," explains William Loomis, a professor of biology at UCSD and one of the key members of the international sequencing effort. "Specialization appears to lead to loss of genes as well as the modification of copies of old genes. As each new genome is sequenced, we learn more about the history and physiology of the progenitors and gain insight into the function of human genes."

The highlighted part shows that randman's conclusion is, as usual, wrong.

And I'm not convinced this was the guy's official conclusion. It sounds an aweful lot like what you get when a reporter interviews a scientist. There's simply no way the guy didn't know about double-crossovers. So what we're getting from randman is a cherry-picked quote from among cherry-picked quotes.

Dictyostelium usually exists as a single cell organism that inhabits forest soil, consuming bacteria and yeast. When starved, however, the single cells come together, differentiate into tissues and become a true multicellular organism with a fruiting body composed of a stalk with spores poised on top. This increases its utility in a variety of studies.

You know what this sounds an aweful lot like? An intermediate form. You know, those thigns which don't exist?

He and the other members of the international sequencing team found that there are more protein coding genes in the organism than they had thought and nearly twice as many as there are in fungi. Their unraveling of the genome also allowed Rolf Olsen, a postdoctoral fellow working in Loomis' laboratory, to generate a tree of life and show that amoebozoa, the group to which Dictyostelium belongs, evolved from the common ancestor of eukaryotes (the group of organisms that contain all animals, plants, algae, protozoa, slime mold and fungi) before fungi. Dictyostelium has about 12,000 genes that produce a greater variety of proteins than the approximately 6,000 found in fungi. And its genes are more closely related to human genes than are the genes from fungi.

Another relevant quote--they simply don't talk about animals and plants. They talk about fungi.

 

[A'isha]

And I'm not convinced this was the guy's official conclusion. It sounds an aweful lot like what you get when a reporter interviews a scientist. There's simply no way the guy didn't know about double-crossovers. So what we're getting from randman is a cherry-picked quote from among cherry-picked quotes.

Here is the actual 2005 paper that the journalism article was about. Randman, naturally, didn't bother to go looking for that, instead relying on cherry-picked quotes yet again (he actually brought this exact same quote up back on page 4 of the big thread in Religion and Philosophy, though he didn't give the source then).

The reason why he didn't bother to go straight to the source is probably because, surprise surprise, it was talked about (typically late after the actual discovery) on Uncommon Descent. They use that journalism article (and Dr. Loomis' quote) as evidence for front-loading, too.

And, as usual, actual scientists don't seem to think this development is a harbinger of the end of evolution any time soon, contrary to what randman and Uncommon Descent are desperately wishing. A search on PubMed for peer-reviewed papers using the term "Dictyostelium genome" returns almost fifteen hundred results (74 pages at 20 results per page!). 15 of those pages, or almost 300 papers, were published just since the original announcement.

Once again, the reaction to the scientific community is not "NOOO! Evolution is ruined! Ruuuuuined!" but "Sweet! Check out this new toy to play with that tells us so much more about evolution than we knew before!"

And thus, science marches on, leaving randman and people like Davison and the other bloggers at Uncommon Descent still waiting for the Final Once And For All Collapse Of Evolution Coming Any Day Now.

EDIT: Hysterically, the Common Descent blog entry about this even says "I googled up the one [ie, the link to the journalism article] above without really doing more than skimming it."

 

[randman]

Nothing in that paper disagrees with what I posted and he said.

"The cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals," explains William Loomis, a professor of biology at UCSD

 

[A'isha]

Nothing in that paper disagrees with what I posted and he said.

You just don't understand what he was saying. You think he's saying that the ancestor organism had more types of genes as a whole than either modern plants or modern animals. What he's actually saying is that the ancestor organism had some plant genes that modern animals don't have, and some animal genes that modern animals don't have. It, however, didn't have most of those other plant-only and animal-only genes that evolved after the lineages diverged, and that therefore the ancestor of the Dictyostelium diverged from the ancestor of plants and animals (and fungi) at a point different from where we thought it did.

You know, just like Acropora millepora, which you also falsely tried to imply scientists were coming around to the front-loading idea due to evidence showing a different divergence point thanks to genomic evidence.

Why don't you ask Dr. Loomis yourself if he believes in front-loading due to what he learned from the sequencing of the Dictyostelium genome?

 

[randman]

You think he's saying that the ancestor organism had more types of genes as a whole than either modern plants or modern animals. What he's actually saying is that the ancestor organism had some plant genes that modern animals don't have, and some animal genes that modern animals don't have. It, however, didn't have most of those other plant-only and animal-only genes that evolved after the lineages diverged

Prove it.

 

[A'isha]

Prove it.

You're the one who brought up Dr. Loomis' quote, claiming to know what it meant (specifically regarding front-loading).

You prove it. I already told you the easiest way to do that.

 

[Dinwar]

Nothing in that paper disagrees with what I posted and he said.

Oh, sure, he never directly stated "This statement is wrong". However, 1) you didn't read the real article, or at least present no evidence that you have, and therefore YOU DON'T KNOW what he said (remember, reporters are not honest when it comes to evolution) and 2) the REST OF THE ARTICLE disagrees with pretty much everything you say. Including, I must repeat, presenting a transitional form, one of those things you suggested multiple times don't exist.

You're playing pathetic linguistic games.

Secondly, you obviously don't understand what's being dealt with here. Scientists aren't looking at the last common ancestor, but an organism that decended from the last common ancestor. It has as much evolution under its belt as we do. Sure, a scientist speculated that it appears that the last common ancestor had a very complex genome. However, that's all this is--speculation. Worse, it's speculation that's been cherry-picked out of cherry-picked quotes. You demonstrated that you can make Gould sound like a Creationist by cherry-picking (and you're not particularly good at that either, by the way--I've seen MUCH better). Imagine just how much damage you can do to a quote with multiple cherry-picking events.

One might say you're selecting the statement you want......

 

[randman]

Prove it then, Dinwar. Show where he didn't mean what his words said. Keep in mind it's not just this one paper.

 

[randman]

You're the one who brought up Dr. Loomis' quote, claiming to know what it meant (specifically regarding front-loading).

You prove it. I already told you the easiest way to do that.

So you cannot prove your claim. You said he was just referring to some types of genes animals and plants don't have today.

What's the basis of that? Your prejudice?

How would he even know if they had genes that don't exist today? His whole argument is we can infer they had more based on what?

Why would he suggest they had more types of genes, for example?

Instead of just assuming he cannot mean what he clearly says, you should explain why.

This is his comment again:

"The cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals," explains William Loomis, a professor of biology at UCSD

You are basically saying they just had different types and so some not present today rather than "more types" which means they also must have had the same types that exist today.

 

[A'isha]

So you cannot prove your claim.

I'm not making a claim, I'm saying your claim is wrong, that it's not consistent with what Dr. Loomis or anyone else involved in any part of studying the genome has said or is saying now. It's certainly not consistent with the way they're treating the genome data, even now, six years later.

I'm asking you to prove your claim.

Not your interpretation, not "well, what else could he mean" insinuations. Prove he meant by those words what you think he meant.

Ask him what he meant by those words.

 

[randman]

I'm not making a claim, I'm saying your claim is wrong, that it's not consistent with what Dr. Loomis or anyone else involved in any part of studying the genome has said or is saying now. It's certainly not consistent with the way they're treating the genome data, even now, six years later.

I'm asking you to prove your claim.

Not your interpretation, not "well, what else could he mean" insinuations. Prove he meant by those words what you think he meant.

Ask him what he meant by those words.

Easy, he says:

Specialization appears to lead to loss of genes as well as the modification of copies of old genes.

 

[ThunderChunky]

Few points. I am not just reading one paper. Look into the matter and you will see what I am saying is true. The LCA of animals is not just predicted to be more genetically complex than worms, and the LCA of plants and animals is thought now to have "more types of genes available" to them than plants and animals have today.

Plenty of what you said has been false, and you have conflated and confused several different issues. When talking about the LCA of animals dont start blabbing about the LCA of plants and animals without some sort of segway.

Do you even know what you are saying? You have provided nothing to support you statement that the LCA of animals was "so complex" other than your misinterpretation of a research paper that you dont understand.

Note this comment (different studies).



http://www.biology-online.org/articles/biologists_determine_genetic_blueprint.html

Just because it had more gene families does not mean it is more genetically complex. You dont understand the words you are using. Like organisms, gene families can also go extinct or be lost in specific lineages.

A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

Nothing that surprising or "extraordinary" as you seem to believe.

The organisms that diverged from the last common ancestor of all eukaryotes followed different evolutionary paths, but all retained the basic properties of eukaryotic cells. Their genomes have been sculpted by chromosomal deletions and duplications that led to lineage-specific gene family expansions, reductions and losses, as well as genes with new functions. Our analysis of Dictyostelium's proteome shows that similar mechanisms have shaped its genome, augmented by horizontal gene transfer from bacterial species.

Similar mechanisms that were already known...nothing extraordinary.

Prove it.

Look at Fig. 6 of the paper. Clearly the majority of the proteins are not present in amoeba, the amoeba just has a few from each of the plant-specific, fungi-specific, and animal-specific groups.

http://img843.imageshack.us/i/pfamdomains.jpg/

Boxed proteins are present in the amoeba, not boxed are absent. Of the plant, animal, or fungi specific the nonboxed number is bigger.