IDiots, the Tree of Life, and phylogenetic trees

Shorter Luskin (comments, not in height): DIFRENT JEANS MAEK DIFRENT TREAHS TEHEREFORE JESUS!!! DIRP!

You know how we always laugh at the fact Creationists dont ever have degrees in biology? This illustrates one of the many, many times it would be handy for Caseytits to have taken a couple bio classes in college.

Darwins Tree of Life is a metaphor. It is very clearly a metaphor in Origin of Species:

The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have at all times overmastered other species in the great battle for life.

Darwin didnt know shit about DNA or phylogenetic analyses. He didnt know how, but maybe, just maybe, all species are related, thus connected– like branches of a tree. And maybe this means we all came from the same seed– one universal common ancestor.

The general idea of Darwins ToL is still 100% accurate. We are all ‘related’ to every other living thing on this planet. But we know now we probably didnt come from *one* LUCA, but probably lots of LUCAs swapping genes around through horizontal gene transfer. Gene soup. heh.

Now, what is a phylogenetic tree? These trees are not metaphorical. They are graphical representations of genetic similarities/differences between your input sequences. The ‘tree’ you get out the end of your analysis is one of many possible ‘trees’– usually the program you use to make these gives you, say, the top 5 most likely trees. When we do this with viruses, we might get a tree like this:

We can see HIV-1 clusters with the SIV from chimpanzees, so we probably got HIV-1 from them. HIV-2 clusters with SIV from sooty mangabeys, so we got it from them. And all HIV/SIVs cluster together, while FIV sits as more of an outsider.

Yay.

But whats this Caseytits says about ‘different genes, different trees of life’? Well, lets assume Caseytits meant ‘different genes, different phylogenetic trees’. Well DUH. Every gene has its own evolutionary history. Lets look at three trees from one paper– ‘Genetic and phylogenetic evolution of HIV-1 in a low subtype heterogeneity epidemic: the Italian example‘.

The first tree they made used env. The env gene is under intense selective pressure from the environment (your immune system), and the Env protein can tolerate very high levels of mutation, thus when they made a phylogenetic tree of their patient sequences, they got this tree:

They next made a tree with pro (part of pol). Pro has its own evolutionary problems to deal with: protease inhibitors. Pro was sitting pretty till we invented those bad boys.

They then analyzed gag, a gene that actually has something called a ‘major homology region’– even distantly related HIV-1s have the same sequence. Its critical, so things dont like to change much here unless they have to (MHC I).

OH MY GOD!

OH MY GOD!

Three different genes, THREE DIFFERENT TREES!

If we believe Caseytits logic, this means that HIV-1 is not transmitted from person-to-person. HIV-1 is specially created in each infected individual, thus genetic comparisons between patient isolates of HIV-1 are impossible, which is why three genes=three trees.

Or, you could understand that each gene has its own evolutionary history, thus trees constructed from each gene need to be taken into the appropriate context. You might also notice that these patient Subtype B sequences, though they create different trees, always cluster with… Subtype B. They never clustered with Subtype A or D or any other, in any tree.

Just like we never construct a ‘human’ phylogenetic tree and see we are more closely related to ‘chickens and cows’ than we are to chimpanzees.

Pay attention in school, kids. Drink your milk. Dont grow up to be a little IDiot.

Comments

#1 Joshua
May 11, 2009

If we believe Caseytits logic, this means that HIV-1 is not transmitted from person-to-person. HIV-1 is specially created in each infected individual, thus genetic comparisons between patient isolates of HIV-1 are impossible, which is why three genes=three trees.

Of course HIV is specially created in each SINNER who contracts it! Because GOD is punishing them for SINNING, of course! That’s why the Pope says that condoms cause AIDS, because when you have sex with a condom you MURDER all those poor spermies, so GOD has to mix up a new batch of HIV just for you. He really gets bored of making all these new, specially-created HIV strains that are all tailored specifically to each individually, which is why he hates it so much when people SIN and make HIM infect them with HIV.
#2 BaldApe
May 11, 2009

By an amazing coincidence, I just read this on PZ’s blog.
#3 Raimund
May 11, 2009

Thanks Abbey, your description of the trees for different genes is helping my understanding of the concept of the individual gene as the vehicle of selection that I’m learning about in the Extended Phenotype. You do a great job in describing genetics.
#4 cprs
May 11, 2009

He’s right about Haeckel – Futuyama’s text for one has reproduced his ancient fraud. (Exposed here, Anatomy and Embryology, 196(2):91–106, 1997)

Seems a bit of a leap to claim his rudimentary requote of a NS article on problems of phylogeny contruction implies he would be obliged to consistently hold HIV quasispecies were specially created.

What do posters here make of

convergence problems in constructing viral phylogenies?

J J Bull et al

It’s an older paper I grant.
#5 Eric Saveau
May 11, 2009

He’s right about Haeckel – Futuyama’s text for one has reproduced his ancient fraud.

Haeckel oversimplified for illustrative purposes; he did not commit fraud. That’s a very old and long discredited creationist lie. Haeckel was later found to be wrong about several other things, but that’s true of everyone who was practicing science in the nineteenth century, and will be true again. Funny thing – it’s always the scientists who find and correct scientific error, never creationist idealogues.
#6 Keith Sader
May 11, 2009

Aieeee the stupid, it burns!!!!
#7 Optimus Primate
May 11, 2009

Funny thing – it’s always the scientists who find and correct scientific error, never creationist idealogues.

Slam and dunk. What blows my mind is when the creationists I bicker with on a daily basis pull this out as if it were some sort of weakness of science.
#8 Anton Mates
May 12, 2009

cprs,

He’s right about Haeckel – Futuyama’s text for one has reproduced his ancient fraud. (Exposed here, Anatomy and Embryology, 196(2):91–106, 1997)

If by “right” you mean “wrong.” The study you cite did not find that Haeckel had committed intentional fraud, and did find experimental support for von Baer’s law. The authors of that study also wrote a letter to Science the following year (15 May 1998: Vol. 280. no. 5366, p. 983), in which they stated:

Data from embryology are fully consistent with Darwinian evolution. Haeckel’s famous drawings are a Creationist cause célèbre. Early versions show young embryos looking virtually identical in different vertebrate species. On a fundamental level, Haeckel was correct: All vertebrates develop a similar body plan (consisting of notochord, body segments, pharyngeal pouches, and so forth). This shared developmental program reflects shared evolutionary history. It also fits with overwhelming recent evidence that development in different animals is controlled by common genetic mechanisms.

and closed with:

Haeckel’s inaccuracies damage his credibility, but they do not invalidate the mass of published evidence for Darwinian evolution. Ironically, had Haeckel drawn the embryos accurately, his first two valid points in favor of evolution would have been better demonstrated.

Furthermore, Futuyma’s textbook presents Haeckel’s drawing in a historical context, and explicitly states that Haeckel’s view was largely incorrect. But other than all that, Luskin was completely right!

Seems a bit of a leap to claim his rudimentary requote of a NS article on problems of phylogeny contruction implies he would be obliged to consistently hold HIV quasispecies were specially created.

Why? If the fact that different individual genes produce different trees is enough to “annihilate the tree of life”, as Luskin suggests, why shouldn’t that be true for common descent within an HIV-1 population?
#9 Ritchie Annand
May 12, 2009

Need I even mention that rhesus monkeys have an Rh system? Oh my GOD, there are gene trees that keep separate in two different species, therefore common descent is somehow wrong therefore Jesus.
#10 Brian X
May 12, 2009

Fox isn’t even trying anymore. Not that they ever really did.
#11 cprss
May 12, 2009

Richardson’s comments in the Times of London, 11 August 1997, p. 14. ‘This is one of the worst cases of scientific fraud. It’s shocking to find that somebody one thought was a great scientist was deliberately misleading. It makes me angry. What he [Haeckel] did was to take a human embryo and copy it, pretending that the salamander and the pig and all the others looked the same at the same stage of development. They don’t. These are fakes.’

It’s consistent with what he later wrote in Science (under the duress of being labelled a creationist).
He’s a lecturer at my old med school.

Why has Futuyma since apologised for publishing faked photos (unwittingly)?

Evolutinary biology as disctinct form other allied disciplines is a strange science. Would molecular biologists, virologists or geneticists reproduce findings which had been publically exposed as frauds for years? Surely not.

Haeckel by the way was a most unsavoury character and much more can be said about this pioneer of the discipline.
#12 Stephen Wells
May 12, 2009

If cprss would like to take some deep breaths and wipe away the spittle, please note that embryology does not rely on Haeckel’s work. Von Baer published _earlier_. And you might care to look at some modern textbooks which will give you _actual photos_ of embryos for comparison. Arguing with outdated “authorities” is a classic bad habit of creationists.
#13 ERV
May 12, 2009

cprs– Haeckel by the way was a most unsavoury character and much more can be said about this pioneer of the discipline.

So why dont you go on over to PZs blog to bitch about Haeckel instead of derailing my post on phylogenetic trees?
#14 Rev. BigDumbChimp
May 12, 2009

Shorter Luskin – squeeeeeeeek
#15 Prometheus
May 12, 2009

I think god’s littlest lawyer just hates trees.

His parents probably tore up his Heather Locklear pin-up and replaced it with one of those awful Gildonco “Bible Family Tree” posters.

Mother Luskin:”Try masturbating to that Mr Filthy brain!”

Littler Casey “But mooooom, I wasn’t I swear to God!”

Mother Luskin: “BLASPHEMER!!!!!!”
#16 Equisetum
May 12, 2009

Your phylogenetic trees look more like mycelia to me.
#17 Prometheus
May 12, 2009

Ugh.

I just read the final installment of Luskin’s “A Primer on the Tree of Life”. I don’t recommend it. I now feel like a weasel peed in my ear.

He blabbered out twenty pages and twenty three foot notes in order to reach this novel conclusion:

“For those open-minded enough to consider it, common design is a viable alternative to common descent.”

Translation:

“I like magic better.”

What an oily and insufferable pipsqueak.
#18 Glen Davidson
May 12, 2009

Of course it’s BS, but by taking the offensive he’s able to ignore the fact that all of the trees tell of a non-telic evolution of life, with fairly small variations (fish and fowl are never found to be closely related). That’s really the point of IDiocy, to ignore what the inferences from the data, by smothering the important information with cavils over relatively minor details.

And crucially, most IDiots don’t deny language evolution due to borrowings, convergences, etc. Whether Casey’s one of the ones who accepts the plain evidence of language evolution or not, I don’t know, but he’s speaking for some who do. It’s completely mindless to accept the cause and effect explanation for language evolution, and then to refuse the non-design causes for the effects in biological evolution.

To be sure, the bleat about language evolution would be that it is “designed”–although mostly it is not. But that’s the answer to the wrong question in the first place, because what is important is epistemology, and we are able to basically show that the effects found in language evolution match up with what we know of the “human mind.” As important, we know that the effects found in biological evolution do not match up with the activities of the “human mind,” rather with mindless processes.

Casey fails again, however that has never stopped him.

Glen D
http://tinyurl.com/6mb592
#19 Anton Mates
May 12, 2009

It’s consistent with what he later wrote in Science (under the duress of being labelled a creationist).

Nobody labeled Michael Richardson a creationist (except, maybe, creationists.) To the contrary, any number of biologists have expressed their appreciation for the work of Richardson et al. in digging up evidence of Haeckel’s malfeasance. They’re well aware, as Richardson is, that this doesn’t affect the validity of modern evolutionary theory, but it shines significant light into one corner of historical science.

Why has Futuyma since apologised for publishing faked photos (unwittingly)?

They’re not photos, and why would he apologize for explaining how Haeckel was wrong? As Richardson et al. write, “Haeckel’s drawings are used in many modern textbooks, but not always as primary evidence for evolution. In Molecular Biology of the Cell (the textbook written by Alberts et al.,), the drawings are used mainly to support hypotheses about the stages of development acted on by natural selection. It is only in this limited context that we have reservations about the implications of the drawings.”

Futuyma is not using Haeckel’s drawings to support any such hypothesis. If you want to use Richardson’s work to complain about Alberts, then complain about Alberts—although those more familiar with his textbook have discussed the issue here, and don’t find him to be particularly unqualifiedly supportive of Haeckel either. But Futuyma’s certainly not doing that, and neither do the vast majority of current biology textbooks. If you disagree, please find the ones that do.

Would molecular biologists, virologists or geneticists reproduce findings which had been publically exposed as frauds for years? Surely not.

Are you kidding? There’s a high probability that Mendel fudged his data, and many of the “experiments” Galileo’s traditionally thought to have done were, at best, hypothetical experiments he would have liked to do but didn’t—he wasn’t always clear on which ones he’d actually completed and, if so, what his precise results were. Does that mean that no one ever draws on Mendel or Galileo in genetics or physics textbooks? Of course not. Their work is still pedagogically valuable, and their results have either been disproved long ago or confirmed a thousand times over by other scientists using better methods and equipment. We don’t need them to have done everything right—we’re not using them either as primary data sources or as exemplars of the perfect scientist. Ditto for Haeckel.

Haeckel by the way was a most unsavoury character and much more can be said about this pioneer of the discipline.

Sure—in a lot of ways (positive and negative), he was to the early supporters of evolution what Agassiz was to the scientific creationists. But personal details about either of them don’t particularly bear on whether evolutionary theory is correct.
#20 windy
May 12, 2009

There’s a high probability that Mendel fudged his data,

Not really
#21 SGJM
May 12, 2009

I wish Casey would learn to interview without screaming.
#22 Joshua Zelinsky
May 12, 2009

Interesting also that Casey mentions the New Scientist article. People predicted in advance that that article and (especially its headline) would be used by anti-evolutionists. It is fascinating to see this prediction once again verified.
#23 Azkyroth
May 12, 2009

Caseytits

Now THAT’s a mental image I didn’t need. >.>
#24 Giblet
May 13, 2009

I don’t understand what the creationists find so hard about this concept. Using the 3 gene examples given, you could use the analogy of a clock: the hour hand, minute hand, and second hand all move at different rates but are all driven by the exact same mechanism (obviously I’m oversimplifying, but complexity doesn’t seem to get through to IDer’s very well.) By ID standards since the three hands move differently, then Jeebus must be using the zombie magic to make it happen, because *obviously* there couldn’t be a single process driving these different changes.
#25 Anton Mates
May 13, 2009

There’s a high probability that Mendel fudged his data,

Not really

I should have added,”whether consciously or not.” I was thinking of what your linked paper describes as “unconscious bias in classifying ambiguous phenotypes, stopping the counts when satisfied with the results, recounting when the results seem suspicious, and repeating experiments whose outcome is mistrusted.”

Which I think was largely the case for Haeckel as well. An extremely self-confident man, philosophically inclined to trust his mind’s eye over his real ones, working on objects pretty close to the limit of tech-assisted human vision at the time, he knew what the things he was drawing should look like, so he drew them that way. (Radiolaria as well as embryos.)
#26 cprs
May 13, 2009

Anton, this line or defence sounds a little like a QC spokesman for the VA! Haeckel was fraudulent, Richardson was justly angry. Textbooks and museums have reproduced his distorted diagrams for years even since the exposure (usually relying on photo reproductions)! If you don’t think Richardson was intimidated by providing ‘ammunition’ for creationists, might I suggest you write to him and let us know his answer here? As to whether cases of fraud serve genuine science and whether they are ever now acceptable or useful I leave to that to others to judge. Sounds like a case for uncleaned colonoscopes to me.

But the meat of this post is about the New Scientist article
Bapteste’s quote again was “For a long time the holy grail was to build a tree of life. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded.” And again in a line reminscent of the VA and to remind us its shareholders haven’t changed hands the NS editorial later reassures its readers “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…”! despite the fact its entirely consistent with what critics of evolution’s dogmatic misotheism have been claiming for years, namely that trees of descent are not real, beyond small gene impoverishing steps.

The root of much of Bapteste’s statement is based, as Abbie reminds us, on HGT (horizontal gene transfer) an assumption based on the incompatibility of the data with phylogeny. http://www.pnas.org/content/105/44/17023.full

The gaps in the phylogenetic charts look eerily familiar to those with an interest in CERVs.

“Notwithstanding this possible case of transposase exaptation, we can reject the hypothesis that the extreme level of SPIN sequence identity among widely divergent tetrapods reflects the systematic action of purifying selection. Thus, the only plausible scenario is that active and nearly identical SPIN elements were introduced horizontally, and relatively recently, into several tetrapod species” (My emphasis.)

Pass the blinkers, someone.
#27 cprs
May 13, 2009

By the way, Anton, I share your distaste for Agassiz’ racist ideas and his ‘polygenic creationism’ is an ugly and foolish synthesis.
#28 slpage
May 13, 2009

“Phylogenetic charts”?

At first, I thought we might have an informed critic on our hands. Now I see we just have someone good at regurgitating what they’ve read at various IDcreationist blogs and websites.
#29 slpage
May 13, 2009

As for the Bull paper, I noticed immediately that the title indicated that the viral convergence was “exceptional”.

Further, if/when horizontally transferable elements are identified, an obstacle to more precise phylogenetic tree reconstruction has been removed.
#30 Prometheus
May 13, 2009

“You see Darwin was wrong because that rudimentary phylogenetic sketch of his doesn’t even have a branch for Mycoplasma hurf durf….when the evolutionist frauds tried to correct that in the late nineteenth century but they thought they were a fungus! Morphology harrumpf hurf durf……..Now hand me down that 1898 copy of Über unsere gegenwärtige Kenntnis vom Ursprung des Menschen cause I am going to try and cram it in my puter and get it to poop out a splits tree super network. If it won’t, then all glory to the Discovery Institute, Slytherin wins the house cup!”

Quit it.

Please.

The Prussian Romantics gave us two world wars and screwed with every discipline and aesthetic aspect of human culture for sixty plus years. Let’s let Ben Stein and Casey Luskin keep hunting for truffles in that mine field and move on.

By jibbering about Haeckel you guys are ignoring Little Lawyer Luskin’s goal.

To wit: because of disparities between “molecular and morphological phylogenies” common ancestry is demonstrated to be an baseless ideological fraud and evolution a religion.

He isn’t after the tree, its just a model. He is after LUCA. He wants to kill our Paleoarchean Granny.
#31 Shrunk
May 13, 2009

cprs:

The gaps in the phylogenetic charts look eerily familiar to those with an interest in CERVs.

I”m surprised you’re still harping about the CERV’s after you have already been shown (in the “Zaboomafoo Part 2″ thread) that these present no problem whatsoever for common descent.
#32 Amadán
May 13, 2009

Slytherin wins the house cup!

Hmmm. I can see the evil cabal of the DI as Slytherin, with Casey as its ~~caterpillar-brow~~ snake-tongued spokestroll.

But who shall we cast as the not-terrifically bright Hufflepuffs?

PS Bags I get to be Mad-Eye Moody
#33 Prometheus
May 13, 2009

As if this was not already derailed……

I didn’t know Tree View was a free app with registration.

Cool.

Thanks Kitty Cat Immunodeficiency Virus Researcher Dudes!

Meow.
#34 GaryB, FCD
May 13, 2009

Any chance we can get the attack gerbil’s face off the front page? Or at least draw a mustache or something on him. His face just scared my cat off my lap.
#35 Prometheus
May 13, 2009

“But who shall we cast as the not-terrifically bright Hufflepuffs?”

They live here:
http://www.oprah.com/entity/oprahsbookclub
#36 JimNorth
May 13, 2009

Caseytits. *barf* I prefer Caseyitis. Really, I do. I want my view of tits to be Casey-free, thank you.

Also, Selma Hayek sports a better looking uni-brow.
#37 Anton Mates
May 13, 2009

cprs,

Textbooks and museums have reproduced his distorted diagrams for years even since the exposure (usually relying on photo reproductions)!

Really? Which textbooks and museums contain photo reproductions of Haeckel’s diagrams, and what do they say about those diagrams? Futuyma, as we’ve seen, doesn’t say what you thought he says. What about the others?

If you don’t think Richardson was intimidated by providing ‘ammunition’ for creationists, might I suggest you write to him and let us know his answer here?

You didn’t say Richardson was criticized for “providing ammunition for creationists,” you said he was “labeled a creationist.” Remember?

despite the fact its entirely consistent with what critics of evolution’s dogmatic misotheism have been claiming for years, namely that trees of descent are not real, beyond small gene impoverishing steps.

Everything is consistent with what creationists claim; that’s how you know they’re not doing science. Heck, contrary to your position, some ID guys like Michael Behe are quite happy to say that trees of descent are real.

Now, have you a specific hypothesis about the development of life, which makes predictions about how phylogenetic methods will fail? That bit about “beyond small gene impoverishing steps” sounds promising; are you claiming that phylogenetic methods will recover accurate trees of descent within sufficiently small or young taxa, and that the synapomorphies on these trees will always be gene losses? That, at least, is something you could check against the research literature.

The root of much of Bapteste’s statement is based, as Abbie reminds us, on HGT (horizontal gene transfer) an assumption based on the incompatibility of the data with phylogeny. http://www.pnas.org/content/105/44/17023.full

It would really help to read the paper you cite. Not only does it not say that the data are “incompatible with phylogeny”—whatever that means—it also provides positive evidence for specific transfer events:

“For the opossum lineage, we used ancient repeats found at orthologous positions in opossum and wallaby, which diverged ≈76 mya. Based on the number of substitutions per million years, we infer that both full-length and MITE SPIN families amplified within a fairly narrow evolutionary window (≈31–46 mya) in the lineages of rodents, bushbaby, tenrec, and frog, consistent with a single wave of germ-line infection of diverse tetrapods (Fig. 3). The burst of SPIN amplification seems more recent in the bat and opossum lineages, ≈15 mya (Fig. 3), which may indicate more recent SPIN transfers in these lineages or a delay in their amplification following the initial horizontal introduction.”

Have “critics of evolution’s dogmatic misotheism” been claiming for years that there was a wave of transposon infection across diverse tetrapod species 30-50 mya? If Hovind or Dembski gave a lecture on the topic, I must have missed it….
#38 anonymous pseudonym
May 13, 2009

“Caseytits

I know that my opinions as a male are unfortunately irrelevant in judging what is ‘sexist’, but, nevertheless, it seems to me that adding a slang term for a delightful part of human female anatomy to Casey Luskin’s name is not an efficient, or non-sexist, way to disrespect him. If anything, associating Mr. Luskin with female anatomy is either an insult to women everywhere, or makes Mr. Luskin more intrinsically interesting – and I sincerely doubt that either of those is your intention.

I think that referring to Mr. Luskin with such terms as ‘idiot’, ‘swaggering buffoon’, ‘nattering nobody’, ‘fool’, ‘self-deceiving self-centered incompetent’, and ‘the most convincing argument for unintelligent non-design’ is sufficiently accurate and does not unnecessarily bring in the rather odd presumption that having female anatomy, or having a female anatomical term appended to your name or description, is somehow derogatory.
#39 W. Kevin Vicklund
May 14, 2009

The background for Caseytits

Scroll down to the picture, read the 3 preceding paragraphs.
#40 386sx
May 14, 2009

Those two were talking right past each other. I think Ducey got a little too “creative” with the questions that were fed to him by Luskin. So Ducey asks one question, and then Luskin asnwers answers another, and neither one of them seems to notice, or care.
#41 a lurker
May 14, 2009

Since Futuyma is being tossed around, let me quote from the second edition, page 303:

Haeckel’s belief that each embryonic state reprsents the adult stage of one of its ancestors is flatly wrong (Gould 1977)

He goes on to state that von Baer was closer to the truth, but then points out cases where even his law is not true.

Getting back to the subject. That “gene trees” my not exactly correspond to “phylogenetic trees” is hardly classified or even mysterious and is covered in detail by such utterly obscure authors like Richard Dawkins. No one has heard of him? I wonder if one took the type A blood protein of a human with an AA blood genotype, the type A blood protein of a chimp with an AA blood genotype, and the B blood protein of a human with a BB genotype; did the analysis and found the first human and the chimp where closer than the two humans that dear old Casey would go “OMG, evolution disproved!”

Just seeing that video made my blood boil. Anyone who has even done any reading on the subject knows that he is full of it. I don’t think we can attribute it to mere ignorance like we can for most of his “sheep” — Luskin is acting deceitfully. It must have really tried Abbey’s patience to be stuck in a room with the guy for two hours.
#42 a lurker
May 14, 2009

I messed up the blockquote in my last post. Only “Haeckel’s belief that each embryonic state reprsents the adult stage of one of its ancestors is flatly wrong (Gould 1977)” is a quote. The rest is my words.
#43 Anton Mates
May 14, 2009

cprs,

One other point on your question,

What do posters here make of convergence problems in constructing viral phylogenies?

J J Bull et al

As slpage mentioned, Bull et al. do characterize this problem in their phage lineages as “exceptional,” and provide a few reasons why this is the case:

Three properties of the design may have led to the high rate of convergence, all of which are atypical of what is thought to apply to most organisms:

1. Replicate lineages were exposed to nearly identical selective environments.
2. Strong, mass selection was operating on very large populations.
3. The replicate lineages started with virtually identical genomes.

There is also, of course, the possibility that they weren’t using the best phylogenetic method for the job. I’m not qualified to judge that, but it’s certainly possible that (say) a maximum parsimony search, or a maximum likelihood search under a different sort of substitution model, would have more success.

That said, even if this issue did recur w.r.t a wide range of taxa and phylogenetic methods, that could hardly be evidence against common descent. After all, what Bull et al. have provided is a case where a standard phylogenetic method failed, yet we know from direct observation that the viruses did descend from a common ancestor! If anything, this shows that disagreements and errors in tree reconstruction don’t imply that the underlying hypothesis of common descent is wrong.

So I’d say you’ve actually found a rather good argument, in the form of this paper, against Casey’s position.
#44 Anton Mates
May 14, 2009

Sorry for the double-post–and also, the second blockquote was supposed to end after the “1….2….3…” list. Oh well.
#45 anonymous pseudonym
May 15, 2009

“The background for Caseytits
Scroll down to the picture, read the 3 preceding paragraphs.”

I read it. I scrolled down. I read the 3 preceding paragraphs again. I have no idea what “‘TITS or GTFO’” means, or how it was interpreted by whomever it was said to, or why it was said in the first place.

I stand by my suggestion that using female anatomical terms as an insult is a really bad idea. There are plenty of accurate and insulting ways to describe Casey Luskin, it is not necessary to use female anatomical descriptions – and considerably clearer if you do not.

(One of the basic problems that the Creationists have is a disrespect for the truth, which shades over into a disrespect for other human beings. We do not need to emulate them by implying that being female is ‘bad’, nor do we need to inaccurately imply that various Creationists have female anatomy when it happens that they do not.)
#46 Tyler DiPietro
May 15, 2009

Those of you curious about “Caseytits” would probably be helped by the knowledge that our esteemed bloghost in all likelihood hangs out at a few image /b/oards. That is all.
#47 cprs
May 16, 2009

Dear O dear, what a lot of heat. This is the first time I’ve been able to return in a few days, on account of work blog filters and domestic crises.

There’s far too much to respond to properly here.
But in answer to Anton, look at Fuyutama’s 98 text and you’ll find repoductions of Haeckel for which he apologised after NYT brought the fraud to US public attention in 2000.
I can cite other examples of more recent reproductions in museums and texts, but it will take time to lay my hands on them, though I have seen the details.

As to Richardson, having a little acquaintance with him, I am confident that being accused of being a covert creationist, or just as bad providing materials useful to the critique of evolution persuaded him to publish the letter he and his coauthors subsequently wrote in Science. If you doubt it – feel free to write to him and ask him. He is not a creationist, and which creationist has ever claimed he is one, Anton? Bbut I think he like others has been surprised by the unscientific ferocity of adherents of evolutionary orthodoxy.

As to the paper, I don’t dispute HGT (what’s this blog all about?), and the authors provide plenty of interesting evidence in their favour for this particular instance (esp for a DNA pox virus mediated transfer). The point I’m making is simpler and more basic – the commitment to common descent is cast iron, so cast iron that data that might be interpreted in alternative ways leaves ‘no plausible alternative explanation’ – a sure sign of a mental filter.
Incidentally, I may have missed it in my present haste, but the strongest point in your favour (since the truth is the only ideology that matters) hasn’t been made – the sites are not orthologous for SPIN, except in rats and mice.

As to Shrunk’s comment on common descent, I agree that the question of orthologous sites has been addressed and left for further clarification when the genomes are sequenced, but the complete absence of CERV1 and 2 in man and orangutan has only been explained by late cross infection, despite the discrepancy with the dates. The protection against CERV1 you’ve cited is somewhat speculative.
#48 Anton Mates
May 17, 2009

cprs,

But in answer to Anton, look at Fuyutama’s 98 text and you’ll find repoductions of Haeckel for which he apologised after NYT brought the fraud to US public attention in 2000.

Apologies—I misread your earlier post. I thought you were asking why Futuyma didn’t apologize. I haven’t seen an apology myself, but I’ll take your word for it that he did.

So then we have a team of evolution-accepting biologists who published on Haeckel’s faked drawings in a peer-reviewed journal. Science Magazine reports on this research, and quotes other evolution-accepting biologists as saying it’s important and valuable work. Steven Jay Gould writes an article in strong agreement, and both Alberts and Futuyma say that they’ll remove Haeckel’s drawings in future editions of their textbooks. Meanwhile, the vast majority of widely-used biology textbooks continue not to feature the drawings at all, even in the context of criticizing Haeckel’s beliefs as Futuyma had done.

Could you ask for better evidence than this that mainstream biology is not trying to perpetuate Haeckel’s claims, and does not consider them significant evidence for evolution?

I can cite other examples of more recent reproductions in museums and texts, but it will take time to lay my hands on them, though I have seen the details.

Hey, whenever you have time. Remember, the relevant issue to Luskin’s claim is how the reproductions are used–what does the accompanying text say? Are they presented in historical context, or are they alleged to represent the modern understanding of embryonic development?

As to Richardson, having a little acquaintance with him, I am confident that being accused of being a covert creationist, or just as bad providing materials useful to the critique of evolution persuaded him to publish the letter he and his coauthors subsequently wrote in Science.

You’re conflating two different claims again. It’s most definitely true that Richardson was worried about encouraging antievolution propaganda—he explicitly said so in both of his letters to Science. He also alluded to criticisms of Haeckel’s drawinigs which were “religious or political in nature” in his paper, “Haeckel’s ABC of evolution and development.” He deserves kudos for his responsibility in this regard.

But that clearly doesn’t constitute evidence that he was ever accused of covert creationism.

He is not a creationist, and which creationist has ever claimed he is one, Anton?

I have no idea if any have. You were the one who said he’s been labeled a creationist, but you haven’t yet pointed to anyone who’s actually labeled him as such.

But I think he like others has been surprised by the unscientific ferocity of adherents of evolutionary orthodoxy.

I’m surprised you don’t accuse Richardson of “unscientific ferocity,” given that he’s obviously as concerned as anyone about his work getting quote-mined and misused by creationists. I certainly haven’t seen him accuse anyone else of overreacting in the name of “evolutionary orthodoxy.”
#49 Anton Mates
May 17, 2009

As to the paper, I don’t dispute HGT (what’s this blog all about?), and the authors provide plenty of interesting evidence in their favour for this particular instance (esp for a DNA pox virus mediated transfer). The point I’m making is simpler and more basic – the commitment to common descent is cast iron, so cast iron that data that might be interpreted in alternative ways leaves ‘no plausible alternative explanation’ – a sure sign of a mental filter.

The trouble with that argument is, horizontal gene transfer is a very general and open-ended explanation. All it means is that the genes were transferred from one organism to another by some mechanism other than inheritance. Could be viruses, could be microscopic wormholes, could be angels…doesn’t matter, it’s still horizontal. So it’s almost oxymoronic to accuse the authors of a “closed-minded commitment to HGT.” It’s like complaining about someone’s dogmatic insistence that a man currently standing on a street corner probably came there from somewhere else, rather than being born and raised on that exact corner.

There are literally only three possible alternatives to HGT. The sequences in question could have been vertically transferred—that is, inherited from a common ancestor. But the study finds strong evidence against that. The sequences could have developed convergently, but their length and subsequent diversification makes that vanishingly unlikely. Or the sequences could have been transferred from some nonliving DNA source, but until someone finds a giant 50-million-year-old pool of DNA sitting around in a cave somewhere…yeah, that’s not plausible either.

So some kind of HGT is really the only remaining option.

As to Shrunk’s comment on common descent, I agree that the question of orthologous sites has been addressed and left for further clarification when the genomes are sequenced, but the complete absence of CERV1 and 2 in man and orangutan has only been explained by late cross infection, despite the discrepancy with the dates.

And, as we’ve said a zillion times already, the people who generated those dates provide assorted reasons to think they’re probably wrong. If further research provides strong support for those dates, then we’ll have reason to rethink the issue.
#50 efrique
May 18, 2009

Luskin’s problem would be not understanding the difference between a gene and the organisms it sits in.

Two species may share a single gene, for example, or one species might have several versions of a gene.

Consequently, the tree for a gene is not going be the same as the tree for the various species the gene is in, because two species might diverge on a large number of genes but share the gene you’re looking at – that is, in the gene’s tree, the two species will sit together on a branch, whereas on the tree for a different gene (one that’s related but different), they will lie on two different branches. The two gene trees are different, and neither gene tree will look exactly like the tree that is at the species level (of course there will be some similarities, but only some).

Luskin is simply too dopey to figure this simple fact out, that gene trees will be different from each other AND different from the darwin-type tree we’d draw for the species (where branching represents speciation).
#51 W. Kevin Vicklund
May 19, 2009

Why has Futuyma since apologised for publishing faked photos (unwittingly)?

Why do you think he has apologized for publishing faked photos? First of all, they aren’t photos, and secondly, I have yet to see any evidence that Futuyma believes the drawings to be fake. Here is an excerpt from Jonathan Wells Icons of Evolution:

But now he knows that “Haeckel was inaccurate and misleading,” and he said he will take this into account in future editions of his book.

He didn’t say he would stop using the drawings, and in fact went on to say that they were still useful. He pretty much mirrored what we have said here about the drawings.