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Tree of Life cheat notes

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For when life makes a fool of the textbooks.

In Evernote, courtesy a reader, for example:

Tree of Life in tatters: “The problem is rampant in systematics today. An article in Nature reported that “disparities between molecular and morphological trees” lead to “evolution wars” because “[e]volutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”14 Another Nature paper reported that newly discovered genes “are tearing apart traditional ideas about the animal family tree” since they “give a totally different tree from what everyone else wants.”15 So severe are the problems that a 2013 paper in Trends in Genetics reported “the more we learn about genomes the less tree-like we find their evolutionary history to be,”16 and a 2012 paper in Annual Review of Genetics proposed “life might indeed have multiple origins.”17 – See more at: http://www.evolutionnews.org/2014/03/cosmos_episode_083331.html#backfn13

File:Tree of life by Haeckel.jpg
Tree of Life we learned in school

Shouldn’t that be “chips,” not “tatters”? Anyway, he recommends Evernotes for keeping track. Today, you need something just to keep up with all the instances of what’s really happening vs. the bumf:

In 1980, Carl Sagan knew nothing about ENCODE and modENCODE. With all the revelations of genetic complexity coming to light in the past 34 years, these must be hard times for Neil deGrasse Tyson to keep a straight face while sweeping his hand up the cartoon-drawn Tree of Life in Cosmos 2.0 and ascribing “all the beauty and diversity of life” to random mutations. As Casey Luskin noted, it only makes sense if you don’t think about it.

But sometimes we need to think about things.

And he says a system like Evernotes makes it easy to go right through to the original source and read it again in context.

File:Tree of life SVG.svg
Current version of tree

Here’s another collection, including:

“[O]ur ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years” (M. A. Wills, “The Tree of Life and the Rock of Ages: Are We Getting Better at Estimating Phylogeny?,” BioEssays, Vol. 24: 203-207 (2002) reporting on the findings of M. J. Benton, “Finding the Tree of Life: Matching Phylogenetic Trees to the Fossil Record Through the 20th Century,” Proceedings of the Royal Society B, Vol. 268: 2123-2130 (2001).)

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Yet the Darwinists still keep their faith. mrchristo
Querius as to,, "Plus there might be a succession of concentric rings, each more finely tuned for stability than the previous." That was somewhat of my initial hunch as to why Biosphere2 failed. i.e. The stability of the ecosystem becomes much more precarious the higher you build it. Lower level systems being easier to maintain whereas a ecosystem complex enough to support man would have to be extremely finely tuned. bornagain77
ba77, Here are some examples from this fascinating area: 1978 experimental approach - I wonder how sensitive the results are to the initial conditions (butterfly effect) http://www.jstor.org/discover/10.2307/1936578?uid=3739560&uid=2129&uid=2&uid=70&uid=4&uid=3739256&sid=21103735185317 Studying ecological instability from invasive species - I liked this statement: "Researchers in diverse fields have suggested that complex systems do not have single stable equilibria in the long-term due to inevitable perturbation." http://chans-net.org/content/unstable-ecological-economic-equilibria-effects-invasive-species-and-ecosystem-restoration-n A study of biodiversity variation in soils---what's interesting is their broadening their conclusions to general principles. In my opinion, the idiosynchratic result that's referred to is likely to become a positive feedback loop that oscillates until it damages the carrying capacity of the ecosystem. http://www.nature.com/scitable/knowledge/library/biodiversity-and-ecosystem-services-is-it-the-96677163 It might turn out that micro-ecosystems are unstable when they're closed precisely because stability results from geographic expansion---that a ring of stability forms at the edges of the expansion. It might be interesting to test this. Plus there might be a succession of concentric rings, each more finely tuned for stability than the previous. Meditation:
God created man in His own image, in the image of God He created him; male and female He created them. God blessed them; and God said to them, "Be fruitful and multiply, and fill the earth, and subdue it; and rule over the fish of the sea and over the birds of the sky and over every living thing that moves on the earth." Then God said, "Behold, I have given you every plant yielding seed that is on the surface of all the earth, and every tree which has fruit yielding seed; it shall be food for you; (NIV)
-Q Querius
Heh. Thanks. To me, this is what makes science so much fun! Alternatively, one can spend the time making students memorize vocabulary and recite the Darwinian catechism. -Q Querius
Querius, quite the little experimentalist you were! :) bornagain77
ba77 said,
Querius, if you run across that experiment again let me know, that would be an nice addition to the Biosphere2 reference.
Well, I tried. Now I'm kicking myself for not bookmarking it, because I was in a rush but wanted to read it in detail later. I once was able to set up a stable ecosystem back when I was in high school. Here's how it happened. As a biology experiment, I wanted to raise hydra because I thought they were cool looking and predatory. My biology teacher purchased a jar containing a few and I followed the instructions to the letter. The instructions had me put distilled water in a petri dish, add the hydra and some daphnia. Disappointingly, the hydra didn't seem to be competent in catching the daphnia and over the next few days each of the hydra grew smaller and eventually turned into blob that got still smaller until they vanished. The instructions said that hydra sometimes went into "depression." I thought that this was ridiculous, and supposed that the hydra didn't prefer eating daphnia and simply starved. So, I prevailed on my teacher to get some more hydra. I made a tank by cutting off the top of a large glass jug, and filled it with pond water, elodea, and some daphnia. I hoped the pond water would include whatever hydra preferred. Then, I added a few hydra and left the tank in a shady place. The results were remarkable. Over the next few months, my hydra population exploded! I stopped counting when the population exceeded 100. My teacher traded hydra for lab equipment and supplies with all the other high schools in the area, so he was very pleased with our arrangement! In observing the hydra, I noticed that their tentacles stretched all the way across the tank, which was perhaps 24-30 cm (10-12 inches) in diameter, criss-crossing each other. Putting some black paper behind the tank as I shined a flashlight into the tank helped me to see the sparkling, filamentous tentacles that seemed nearly as thin as spider webs. The daphnia, zoomed around in the tank doing their own thing, but I never observed any of them being ensnared by the hydra, which reinforced my hypothesis that hydra fed primarily on much smaller organisms, perhaps even microbes. The hydra tentacles were normally perfectly still. When a daphnia crashed into a tentacle, the tentacle withdrew defensively and did not ensnare the daphnia. My only regret is that I didn't have access to a dissection microscope at the time so I could observe what was happening on the tentacles. In this case, my ecosystem didn't fail, perhaps due to the diversity of life from the pond water. -Q Querius
Another Nature paper reported that newly discovered genes “are tearing apart traditional ideas about the animal family tree” since they “give a totally different tree from what everyone else wants.” So severe are the problems that a 2013 paper in Trends in Genetics reported “the more we learn about genomes the less tree-like we find their evolutionary history to be,”
What bothers me is that so many prominent Darwinists are in denial. They grimly and pugnaciously cling to their dogmas and doctrines, admitting nothing, while generating a smokescreen of speculations and rhetorical arguments as they try to find ways to stuff incompatible data into an old rag-doll theory. This can't be science. -Q Querius
Querius, if you run across that experiment again let me know, that would be an nice addition to the Biosphere2 reference. bornagain77
ba77, Fascinating! But no, this wasn't the one I recently ran across. The one I'm thing of unsuccessfully tried to balance a small number of types of micro-organisms in a closed ecosystem. IIRC, it had a bit of an OOL flavor to it. Still, the Biosphere II experiment further reinforces the "ecosystem as a finely tuned organism" concept over the competitive model optimized with kudzu, killer bacteria, killer fungi (kill 'em now, why wait until they're dead), fire ants, piranha bunnies, and the like. Not a fun place to be. -Q Querius
Querius as to: 'Lately, I came across an article (that I promptly lost) concerning attempts to form simple, stable ecosystems with micro-organisms under lab conditions resulting in oscillating populations that increased in magnitude until the carrying capacity of the ecosystem was damaged, and the populations collapsed.' Are you thinking of Biosphere2 ? Biosphere 2 – What Went Wrong? Excerpt: Other Problems Biosphere II’s water systems became polluted with too many nutrients. The crew had to clean their water by running it over mats of algae, which they later dried and stored. Also, as a symptom of further atmospheric imbalances, the level of dinitrogen oxide became dangerously high. At these levels, there was a risk of brain damage due to a reduction in the synthesis of vitamin B12. http://biology.kenyon.edu/slonc/bio3/2000projects/carroll_d_walker_e/whatwentwrong.html bornagain77
bornagain77 observed
...amazingly you will still find Darwinists defending it tooth and nail as if their life depended on it being true, such as our own evolutionary biologist wd400.
Exactly! What's been disappointing is the apparent lack of any interest in thoughtful discussion by Darwinists. Their attitude seems to be one that requires every discovery from the wilds of nature to be captured, neutered of any disturbing data, and then frog-marched into Darwin's dungeon. However, their Darwinian "Norwegian Blue" parrot is dead. It's an ex-parrot and a deceased theory that should have passed away with the 19th century wooden-masted ships. Instead, we need a fresh beginning and a fresh model that starts with genomic data rather than arbitrarily selected morphological similarities. Adaptation needs to be considered in the context of a finely tuned, feedback-driven ecosystem rather than a model reminiscent of a fiercely competitive, individualistic, industrial-age capitalist system, where each species is like a business fighting for survival and dominance. Also, credible sources for genetic novelty have not been identified---bacteria or viruses that reproduce quickly might be possible candidates for a sort of genetic mutualism with larger, slower reproducing organisms. Lately, I came across an article (that I promptly lost) concerning attempts to form simple, stable ecosystems with micro-organisms under lab conditions resulting in oscillating populations that increased in magnitude until the carrying capacity of the ecosystem was damaged, and the populations collapsed. Many years ago, I wrote a computer simulation with similar results, but I thought it was the fault of my program parameters, that reproduction rates were too static (which might well have been be true), as well as the lack of buffer species, and likely other factors unknown to me. Anyway, I think that new discoveries in biological science can be accelerated once we pry ourselves away from Darwinism and its ideologically contaminated evangelists. -Q Querius
Moreover, even if DNA sequences would have been somewhat cooperative for Darwinists, it would still not tell us anything about how and if species evolved because body plan information is not even encoded in DNA in the first place:
Darwin's Doubt narrated by Paul Giem - The Origin of Body Plans - video http://www.youtube.com/watch?list=PLHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8t&v=rLl6wrqd1e0&feature=player_detailpage#t=290 Intelligent Design: The ambitious aim of Douglas Axe (Biologic Institute) - video http://www.youtube.com/watch?v=pnODSjW0bno Not Junk After All—Conclusion - August 29, 2013 Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. https://uncommondesc.wpengine.com/junk-dna/open-mike-cornell-obi-conference-chapter-11-not-junk-after-all-conclusion/
Verse and Music:
Genesis 1:25 God made the wild animals according to their kinds, the livestock according to their kinds, and all the creatures that move along the ground according to their kinds. And God saw that it was good. Eric Church - Like Jesus Does (Acoustic) http://www.youtube.com/watch?v=wuG1rLPjVkk
Even though Darwin's tree of life is in 'tatters', amazingly you will still find Darwinists defending it tooth and nail as if their life depended on it being true, such as our own evolutionary biologist wd400. Here are a few more notes.
Richard Dawkins: How Could Anyone “Possibly Doubt the Fact of Evolution” - Cornelius Hunter - February 27, 2014 Excerpt: there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.”,,, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”,,, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”,,, he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.” “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.” And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility. http://darwins-god.blogspot.com/2014/02/richard-dawkins-how-could-anyone.html Here Are Those Incongruent Trees From the Yeast Genome - Case Study - Cornelius Hunter - June 2013 Excerpt: We recently reported on a study of 1,070 genes and how they contradicted each other in a couple dozen yeast species. Specifically, evolutionists computed the evolutionary tree, using all 1,070 genes, showing how the different yeast species are related. This tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. Yet one of the fundamental predictions of evolution is that different features should generally agree. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.” In fact, as the figure above shows, the individual gene trees did not converge toward the concatenation tree. Evolutionary theory does not expect all the trees to be identical, but it does expect them to be consistently similar. They should mostly be identical or close to the concatenation tree, with a few at farther distances from the concatenation tree. Evolutionists have clearly and consistently claimed this consilience as an essential prediction. But instead, on a normalized scale from zero to one (where zero means the trees are identical), the gene trees were mostly around 0.4 from the concatenation tree with a huge gap in between. There were no trees anywhere close to the concatenation tree. This figure is a statistically significant, stark falsification of a highly acclaimed evolutionary prediction. http://darwins-god.blogspot.com/2013/06/here-are-those-incongruent-trees-from.html That Yeast Study is a Good Example of How Evolutionary Theory Works - Cornelius Hunter - June 2013 Excerpt:,,, The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene. These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes or of the problem that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.” And how do we know that these genes have strong phylogenetic signal. Because they give the right answer. This is an example of a classic tendency in science known as confirmation bias.,,, http://darwins-god.blogspot.com/2013/06/that-yeast-study-is-good-example-of-how.html Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors. Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,, Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php podcast - Molecular Data Wreak Havoc on (Darwin's) Tree of Life - Casey Luskin - March 2014 http://intelligentdesign.podomatic.com/entry/2014-03-14T16_17_31-07_00 Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885
etc.. etc...
Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013 Excerpt: Although humans and chimpanzees share,, similar genomes (70% per Tomkins), previous studies have shown that the species evolved major differences in mRNA expression levels.,,, http://www.sciencedaily.com/releases/2013/10/131017144632.htm Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F The Mismeasure of Man: Why Popular Ideas about Human-Chimp Comparisons Are Misleading or Wrong - Ann Gauger March 10, 2014 http://www.evolutionnews.org/2014/03/the_mismeasure083011.html
(white space = entire inner white circle) drc466
I love the "current version of the tree". It reminds me of the old "Then a miracle occurs" cartoons - see that big white space in the middle? That's the then a miracle occurs space! drc466

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