Peanut Gallery - AronRa/Enyart - Phylogeny

[Dragan Glas]

Greetings,

YesYouNeedJesus, just out of interest - since you've said you're a YEC - would you care to start a thread in the Creationism/ID forum regarding what you believe to be the age of the Earth and why?

I'd welcome a chat about that.

Kindest regards,

James

 

[)O( Hytegia )O(]

I think I may have forfeited my BIGGEST FAN Award.
=[

True, that award goes to me and me alone!

Side-note:
I'm now reading this in your voice ever since the League Of Reason show talks kicked off.
GET OUT OF MY HEAAAAD

 

[Inferno]

Side-note:
I'm now reading this in your voice ever since the League Of Reason show talks kicked off.
GET OUT OF MY HEAAAAD

Hey, my voice is sexy so shut up!

Awesome though, the only three people who can do that for me are Carl Sagan, Christopher Hitchens and AronRa.

 

[scalyblue]

Side-note:
I'm now reading this in your voice ever since the League Of Reason show talks kicked off.
GET OUT OF MY HEAAAAD

Hey, my voice is sexy so shut up!

Awesome though, the only three people who can do that for me are Carl Sagan, Christopher Hitchens and AronRa.

 

[brettpalmer]

 

[Prolescum]

[centre]

[/centre]

 

[brettpalmer]

[centre]

[/centre]

Well....I (painfully) listened to his radio show today. No mention of the debate with AronRa and I see he hasn't posted in the debate thread yet. But, it's still only 4pm here in Denver.

 

[Inferno]

Wehey, BobEnyart is now registered. Welcome Bob, hope you like it here, let the posting begin!

 

[australopithecus]

I'm not sure what arguing about Newton is supposed to achieve but it sure as hell isn't going to gain any insights into phylogeny...

 

[brettpalmer]

 

[YesYouNeedJesus]

I agree, I'm excited to get into phylogeny as well. But I also would like to see Aron admit his error and we can move on. I'm not sure Aron will be able to do so, but I will hope for the best.

 

[brettpalmer]

I'm not sure what arguing about Newton is supposed to achieve but it sure as hell isn't going to gain any insights into phylogeny...

I was wondering the same thing, but Enyart's opening "argument" is not so much about Newton (everyone in the world could be a creationist but that wouldn't change the fact of evolution) but more about Bob trying to score "gotcha" points.

I was also curious as to why Bob mentioned US doctors who reject "strict" Darwinism (note the qualifying word). Who cares? I wonder if it matters in countering Bob's point if Aron were to pull up a poll of Japanese or Chinese doctors who accept evolution? Enyart could then counter with Turkish doctors who reject "strict" Darwinism. But where does all that get us? :roll:

Hrmph....I was hoping for a better opening post but I guess you get what you get and you don't throw a fit.

 

[YesYouNeedJesus]

Brett, I think Aron brought this one on himself. Especially with this comment: "That way he can dodge the systematic refutation of everything he got wrong, which is everything he said." Ouch...

 

[YesYouNeedJesus]

Greetings,

YesYouNeedJesus, just out of interest - since you've said you're a YEC - would you care to start a thread in the Creationism/ID forum regarding what you believe to be the age of the Earth and why?

I'd welcome a chat about that.

Kindest regards,

James

Yes, pretty soon.

 

[he_who_is_nobody]

I agree, I'm excited to get into phylogeny as well. But I also would like to see Aron admit his error and we can move on. I'm not sure Aron will be able to do so, but I will hope for the best.

Error? What error? AronRa said:

AronRa[/url]"]I don't know if Enyart can show that Newton ever denied any natural explanation in favor of an inexplicable miracle. Neither do I think he can show where Newton wrote 'extensively' about this, not that it would be necessarily relevant to either of our positions. I haven't read Newton myself, but Niel deGrasse Tyson says that Newton never evoked God to explain anything until he came to a point when there were no scientific explanations he could yet conceive.

Emphasis mine, also, start watching the video he linked starting at 8:00 (you should watch the whole video, but that is the point of it).

I guess after AronRa points out BobEnyart's poor reading comprehension, and agrees that Newton was a alchemist and creationist (he was born 155 82 years before Darwin was even born after all), we can move onto phylogeny.

Oh wait:

AronRa[/url]"]

When Pastor Bob Enyart invited me to continue this discussion, he promised that he had an answer to my 'Phylogeny Challenge'. Unfortunately he still doesn't know what the question is. In the preceding portion of this discussion, I asked him to explain it. I expected him to play a clip from the Phylogeny Challenge video,where (from 8:40 on) I explain exactly what the challenge is. Instead, Bob played two separate audio clips from the wrong video, and thought that was it. The clips he played were just statements of fact which contained no challenge. So at the start of part 6, Bob opens on yet another false assumption based on really inattentive research.

Everything we see in nature consistently adheres to everything we would expect of a chain of inherited variations carried down through flowering lines of decent. ...Because the phylogenetic tree of life is plainly evident from the bottom up to any objective observer who dares to compare the anatomy of different sets of collective life-forms. But it can be just as objectively doubly-confirmed from the top down when re-examined genetically."

There is overwhelming testimony from evolutionary biologists that everything you just said is completely wrong, and I have in front of me quotes and specifics. You might claim that I'm taking them out of context, but I'll post the references on this show's summary. I am not taking it out of context. The very day that the testimony was taken in Texas, (I mentioned January 21st 2009) that very day, New Scientist published a cover story on the tree of life. And that cover story goes through the proceedings of the N.A.S. and Nature and Science, and everybody, and it quotes an army of evolutionary biologists who say that genetically the tree of life lies in tatters, that it's being cut down.
Yes, I remember that article because they were talking about the horizontal gene transfer that I brought up in the beginning of the 10th foundational falsehood of creationism.
I know, and I watched that very carefully, but your assertion that genetics covers the tree of life is false, and I can establish that.

No sir. Your reference to, and reliance on, trite sensationalism shamelessly promoted by a popular magazine will not change the fact that genetics has already irrevocably confirmed a network of evolutionary ancestry for many different lineages of life. The reason I referred you to my videos on caniforme and feliforme phylogeny is because both of those videos prove the point, by examining and explaining published peer-revewed genetic analyses:

Mitogenomic analyses of caniform relationships, Science Direct
The Evolution of Cats, Scientific American
Molecular Phylogeny of the Carnivora (Mammalia) - Oxford Journal of Systematic Biology

Likewise my Phylogeny Challenge video also cites several juried papers in peer-reviewed journals:

A Molecular Phylogeny of Living Primates
Human and Non-Human Primate Genomes Share Hotspots of Positive Selection
Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution
A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions
Human-specific loss of regulatory DNA and the evolution of human-specific traits

If you look up each of the listed citations above, you'll see a series of associated studies, none of which could even exist if your 'understanding' of the New Science article was correct. But they do exist, so my point is already proven, and genomic research continues to confirm evolutionary phylogenies.

"Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the genetic level. How are genomes compared and what can these findings tell us about how the overall structure of genes and genomes have evolved? Comparative genomics also provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give each organism its unique characteristics." -Nature (2010)

If these evolutionary biologists are right, then you're wrong, Aron. And genetics tears apart the tree of life, tears it apart. That's why they published a story titled, "Darwin was Wrong on the tree of life".
I remember the story, and I know what it pertains to; it pertained to, -it took the root out of the tree of life.
No! It took the whole branches, the twigs!
No, it took the root!
It slaughtered them!
Just that!
No, you're wrong. You didn't read it. You're wrong. The last time I read it was today. I read the whole article.

Then how did you miss the linked editorial at the very beginning, Uprooting Darwin's tree? In case your subscription isn't up to date, here is an excerpt.

" We now gaze on a biological world of mind-boggling complexity that exposes the shortcomings of familiar, tidy concepts such as species, gene and organism.
A particularly pertinent example is provided in this week's cover story - the uprooting of the tree of life which Darwin used as an organising principle and which has been a central tenet of biology ever since (see "Axing Darwin's tree"). Most biologists now accept that the tree is not a fact of nature - it is something we impose on nature in an attempt to make the task of understanding it more tractable."

How did you miss this part of the article itself?

"Microbes have been living on Earth for at least 3.8 billion years; multicellular organisms didn't appear until about 630 million years ago. Even today bacteria, archaea and unicellular eukaryotes make up at least 90 per cent of all known species, and by sheer weight of numbers almost all of the living things on Earth are microbes. It would be perverse to claim that the evolution of life on Earth resembles a tree just because multicellular life evolved that way.

If there is a tree of life, it's a small anomalous structure growing out of the web of life," says John Dupré, a philosopher of biology at the University of Exeter, UK."

So the article says the phylogenetic tree has no root, just like I said. Obviously I have read this article after all, but it seems you have not. Either that, or you glean for talking points rather than reading for comprehension. You should at least have noticed that the article interviewed two camps; those who say that the tree analogy no longer applies if it can't account for all biota, and the second camp, who say the concept of an 'unrooted' tree still works,at least with regard to animals, if not all other multicellular organisms.

I am sure you're aware that several scientists immediately posted harsh criticism of New Science for their deliberately deceptive title and misleading cover art. The article itself is factually OK, but it is unnecessarily emotive and especially confusing to laymen, obviously. It doesn't explain anything as well as it should have, but it certainly doesn't say what you wish it did either. I know what it's really talking about, and I had already addressed these points months before that article even came out.

Did you see Dennet's reponse?

"Nothing in the article showed that the concept of the tree of life is unsound; only that it is more complicated than was realised before the advent of molecular genetics. It is still true that all of life arose from "a few forms or... one", as Darwin concluded in The Origin of Species. It is still true that it diversified by descent with modification via natural selection and other factors.
Of course there's a tree; it's just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA.
The accompanying editorial makes it clear that you knew perfectly well that your cover was handing the creationists a golden opportunity to mislead school boards, students and the general public about the status of evolutionary biology."

So let me tell you why these evolutionary biologists are saying that Darwin was wrong on the tree of life. Right? Let me give you some of the reasons. This is from the proceedings of the NAS: "European researches examined more than a half a million genes from 181 prokaryotes" (Now I know they don't have a nucleus.) ""¦and found that 80% of them could not be interpreted as forming the branches of a tree of life, 80%. This turns out to be the rule rather than the exception even for eukaryotes, even for organisms that have cells with a nucleus.

At the microbial level, yes it does. However multicellular organisms are better able to protect their genetic core, substantially minimizing occurrence of horizontal gene transfer from 80% closer to 8%.

"Believe it or not, 8% of human DNA is actually old virus DNA. Some viruses, called retroviruses, put their DNA into the DNA of the cells they infect. HIV is a virus like this.
-geneticist, Carrie Metzinger B.Sc., Bergmann Lab, Stamford University

The article also mentions the influence of occasional hybridization and fluke occurrences like a snake bite transferring genes. But these events are so rare and easily identifiable that they do not pose any significant impediment to phylogenetics.

The university of California at Davis has compared 2,000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies, and nemotodes. In theory, they should have been able to use the gene sequences like you claim, to construct an evolutionary tree showing the relationships. They failed. The problem was that the different genes told contradictory stories.
I could spare us some time. It is what I told you at the beginning it was going to be,where it relates to viruses and horizontal gene transfer.
No! No! Were NOT viruses!

I guess your copy didn't include illustrations.

"This is a image of the more or less current tree of life showing the 5 kingdoms and how genetic inheritance is now thought to be not exactly vertical but also includes horizontal gene inheritance via at least virus infection and maybe other routes such as the incorporation of mitochondria and plastids as symbiotic partners within Eukaryote cells."

In addition to the description of the illustration, the article also said this: "40 to 50 per cent of the human genome consists of DNA imported horizontally by viruses, some of which has taken on vital biological functions (New Scientist, 27 August 2008, p 38). The same is probably true of the genomes of other big animals."

Beyond that, the article implies that the reason Syvanen could not construct a consistent cladogram inclusive of all six organisms was because of a bizarre case of horizontal gene transfer at the apparent origin of one of them, turning into a genetic chimera. Remove tunicates from the mix and a cladogram is still easily traceable for the five remaining organisms. In fact, we can still even determine phylogenetic clades for most tunicates.

Just for your amusement:
"Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea."
-BioMedCentral

Now you see that only Appendicularia could not be firmly resolved. Can you explain why Aplousobranchia evolves so much faster than the rest?

I know the article. I know what it means. I already told you"¦
You completely misrepresented what it means. It's about humans. It's about human DNA. That's what the article is about.

No it isn't. It's about how we should abandon the concept of a single universal common ancestor for all forms of life, or even all eukaryotes. It's about whether phylogenetics has become so complex that it can no longer be adequately represented using the analogy of a tree. In point of fact the analogy fails because there is no root, there is no trunk, and of course there are no leaves. As the article said, life doesn't grow vertically either. Only the branching pattern remains, and that is only applicable to multicellular organisms. Even then, there is still a degree of HGT and hybridization which can,albeit rarely- confuse the tree analogy. However,at least with multicellular organisms, hybridization can only occur between two species of the same genus, so even if it happened frequently, it still wouldn't be significant in any protracted depiction. Personally I prefer to render phylogeny as a tumbleweed of life'. I think it is more accurate, and even more helpful in its illustration of evolutionary relationships at least among animals, which is what paleontologists and other folk are most often concerned with. Envisioning phylogeny as a 'tree' is a traditional convention just like your own 'family tree', except the phylogenetic tree is still a much more accurate analogy than the 'tree' in genealogy.

This is my proof that your claim is wrong, that genetics proves the tree. That claim is wrong, and there are hundreds if not thousands of scientists who agree with me.

No there aren't. None of the scientists involved in this article agreed with you. Just to prove that, here is another excerpt from the editorial:

"As we celebrate the 200th anniversary of Darwin's birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that "New Scientist has announced Darwin was wrong". Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not."

I suspect that "an army" consisting of "thousands of evolutionary scientists" don't really agree with you just like "every cosmologist in the world" didn't really agree with you either.

AronRa can just repost this. I cannot wait to see BobEnyart's reaction.

EDIT: Fixed a calculation error.

 

[scalyblue]

AronRa can just repost this. I cannot wait to see BobEnyart's reaction.

We've all seen it already, just with different words out of different mouths. Given bob's first post only seems to contain no assertions about phylogeny aside from "Newton, prior to the discovery of genetics and the codification of evolutionary theory, immersed in a society seeped in religious doctrine, wrote religious texts, therefore young earth hahaha."

To me It's like starting a math debate by presenting as your first proof that since Archimedes didn't know calculus, pi = 3.

If Newton didn't say goddidit when he couldn't explain something, I'm sure we would be much more advanced nowadays.

 

[)O( Hytegia )O(]

Gods.

This is going to be quite interesting...

 

[australopithecus]

If by interesting you mean exactly the same as whenever a creationist tries debate someone who knows what they're talking about; that being piss poor and painful to watch.

 

[)O( Hytegia )O(]

If by interesting you mean exactly the same as whenever a creationist tries debate someone who knows what they're talking about; that being piss poor and painful to watch.

I KNOW!
It's like watching an intellectual version of the movie "Jackass"

:lol:

 

[YesYouNeedJesus]

he_who_is_nobody, Bob's first post is not in reply to Aron's thread here, but to the radio show they did.