W. Ford Doolittle, Cautious Revolutionary with a Chainsaw, and the Tree of Life

MatthewTan, Whether they are programming codes of not, they indicate common descent. jerry

Jerry, I will get Falk's book one day. Now I am reading EoE and Genetic Entropy. The point is the "deletions", the missing letterings, might be real programming codes. The earlier programming code, let say, was abcdefg. And the programming code for humans and apes are ab defg. The "blank" might be part of the code, not deletions. "This is what Darwinist claim except there is a time difference of tens of millions of years as the various species arose." Darwinists claim a progressive "improvement" in genome fitness and complexity. My hypothesis is the reversal, i.e genetic entropy has occurred. MatthewTan

MatthewTan, You should buy Darrel Falk's book (Coming to Peace With Science: Bridging the Worlds Between Faith and Biology). In it he explains pseudogenes, deletions, etc. He also explains a lot of other things relevant to evolution. Deletions are the same sequence as in older species that are still extant but with missing parts to sequence in later arising species. In other words they are identical to what exist in an older species except for a deletion and that same deletion then appears across other later arising species such as chimps and humans. You said "the same genome, eg. all apes (and perhaps even monkey, mice, etc.) and humans started out with more or less the same genome. Then over time, mutations occured to account for the 1% or 5% difference between humans and chimps." This is what Darwinist claim except there is a time difference of tens of millions of years as the various species arose. jerry

Jerry, Johnnyb Now, if SINE and LINE and other "junk" DNA are functional, then: It is a possible scenario that all organisms in high-order taxonomic groups started out with more or less the same genome, eg. all apes (and perhaps even monkey, mice, etc.) and humans started out with more or less the same genome. Then over time, mutations occured to account for the 1% or 5% difference between humans and chimps. The so-called "deletions", "shared errors", and retroviruses (HERV) might not be deletions, errors and viruses at all, but working programming codes. How do they know there were "deletions"? They have assumed that the DNA 3-letter codons convert to amino acids. But if these DNA bits do not code for proteins, then there is no way to ascertain if any these deletions or insertions or errors have occured, unless one knows what DNA sequence code for what function. MatthewTan

johnnyb, I am not sure what you mean. What does "all organisms started out with the same genome" mean? Even if it is a hypothethical. jerry

Just a hypothetical question -- What if common descent is incorrect, yet all organisms started out with the same genome? How would that affect the evidence? Note that the question challenges several assumptions currently present in biology (note that I don't agree with the question, but I think it raises some issues we need to think about). johnnyb

MatthewTan, Thanks for the reference to the Schaer site. I will read what he has to say. The interesting thing is that whether SINEs, LINEs, pseudogenes, deletions, retro viruses etc have functionality or not they are still an example of common descent. Common descent can have an intelligent origin and the fact that these odd sequences appear in multi-species indicate they have a common origin or common descent since they take place over time. If all the DNA in all the genomes has function, that is not contradictory to common descent. jerry

[Off topic] I saw this book on Amazon, The Black Box: Darwin, Marx, Nietzsche, Freud - Stories (Paperback) by Nickell John Romjue (Author) The "Black Box" in the title stands out alluringly. Has anyone read the book? Anything to share? Here's the review: Editorial Reviews Book Description The world today is witnessing the terminal breakup of the great materialist belief systems of the late nineteenth and early twentieth centuries that so powerfully shaped the secular modern mind. No metaphor better encapsulates that breakup of the visionary theories and credos of nature, man, and society advanced by Darwin, Marx, Nietzsche, and Freud than The Black Box. Each of the materialist faiths generated by modernity's famous quartet of founders contained an unknown chamber of surprises, a black box that its author could not, or did not see into. Today the black boxes stand open. First, the intricate cell of life, which the crude optics of Darwin's time could not penetrate, is indisputably a structure designed by intelligence. Second, the hidden component of mass killing that proved organic to Marxist revolutionary regimes. Third, the propensity of Nietzsche's bold vision of trans-moral overmen to produce, not the aesthetic ideal, but cold totalitarian monsters. Fourth, the widespread subversion of individual moral behavior legitimized by the deluded Freudian assertion of the primacy of subconscious drives over the rational mind. In the early twenty-first century, our civilization looks back upon the tragic legacy of materialism: a worldview that declared God to be a human invention, the galaxies and life on Earth cosmic accidents, and morality a factor of need and situation in an aimless universe. God substitutes emerged to fill the void. Religion-hostile National Socialist and Communist party regimes assumed in the twentieth century higher moral authority to kill their unwanted subjects and alien victims on a scale unprecedented in modern history. The stories of this book dramatize the life-crises of five acolytes of the famous four gospels of materialism that so powerfully shaped the violent twentieth century world, along with a sixth who returned on the eve of the millennium for a second look. In these stories, irony and humor could not be avoided. MatthewTan

Jerry,

You are going to have to explain all the common nucleotide sequences that are buried in introns at odd places in the same gene on the same chromosome if you are going to rule out all common descent. The most compelling is the identical deletion sequences. But there are others such as SINEs, LINE’s and retro-viruses.

Have you read this article, How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schaer The article was mentioned earlier on UD here: https://uncommondesc.wpengine.com/intelligent-design/dna-researcher-andras-pellionisz-gives-favorable-review-to-shredding-of-dawkins-and-talk-origins/ Schaer keeps us updated on the functionalities of SINE and LINE and other seemingly function-less DNA bits. "amazing similarities in non functional nucleotide sequences for many species" may be explained by the functions which require the same DNA codes. MatthewTan

jerry, How can you have common descent without phylogeny? Jehu

Jehu, You are going to have to explain all the common nucleotide sequences that are buried in introns at odd places in the same gene on the same chromosome if you are going to rule out all common descent. The most compelling is the identical deletion sequences. But there are others such as SINEs, LINE's and retro-viruses. These all indicate that many separate species most likely had a common ancestor. I have no idea what a phyolgenetic tree has to do with it. People would like to trace it all back to some beginning and have everything nice and neat but sometimes the tracing can only go so far and most times there are dead ends. So a lot of the TOL is wishful speculation. That does not mean you can hand-wave away the amazing similarities in non functional nucleotide sequences for many species. There is no evidence to support the tree of life in the reference you provided so I am not sure why you referenced it. To me all the TOL is question begging. But as I said it does not mean that there is no evidence to trace some species backward through time to some of their ancestors through these non functioning sequences. Now if one could find a function for these peculiar sequences, then that would be interesting. jerry

You are pointing to some problems with universal common descent and I am saying that is different from common descent.

If you would look at the article you will see that the problems are present at every level. I am sorry. I just don't see how common descent can be posited at any level if there is no phylogenetic tree at least at the level where common descent is claimed. Common descent requires phylogeny. If there is no evidence of phylogeny then there is no evidence of common descent, universal or otherwise. Jehu

jerry: "Common descent is just the conclusion that certain species have unusual specific similarities with each other that could not happen by chance and is best explained by having a common ancestor." I think you have identified one of the key points of the issue. Common descent is a reasonable inference from the fossil record, but the mechanism is not in evidence. From an ID perspective it looks something like the progression of human design of technological devices and machines. Common descent is a reasonable inference, but of course this is not proof of any sort. On the large scale of classes and orders and tens of millions of years there appears to be a clear progression, where each new stage of a developmental line is generally an elaboration based on the previous, and multiple new lineages on the order of classes share basic design characteristics with an ancestral line. In other words a vaguely tree-like pattern. This is based on just the fossil record. For me looking at some of the relevant fossil/dating data is persuasive. I think a good example is the progression from primitive jawless fish through amphibians to reptiles: - Ostracoderms (beginning in early Cambrian, 510 Ma); jawless, covered by a bony plate except for the tail region; cartilaginous notochord - Placoderms (beginning in late Silurian, 400 Ma); functional jaws but no teeth, armored over most of body; bony skeleton - Bony fishes (beginning in early Devonian, 390 Ma) - Crossopterygian lobe-finned fishes (mid Devonian, 380 Ma) - Various forms physiologically intermediate between crossopterygians and early amphibians (mid to late Devonian, 380-360 Ma) - First amphibians (late Devonian, 360-370 Ma); quite fishlike - Labyrinthodonts (late Devonian - early Mississippian, 370-350 Ma); larger amphibians with more upright tetrapod characteristics - Anthracosaurs (late Mississippian, 330-320 Ma); early reptiles with some amphibian characteristics - Cotylosaurs (early Pennsyvanian, 320-310 Ma); primitive reptiles with all basic reptile characters Note the tree-like branching at the level of classes, where the "branches" diverged at successive points earlier in time - jawless fish, the lobe fins, the bony fishes, the amphibians, the reptiles. All of this gives a strong appearance of common descent. Each successive "branch" is evidently based on the common design characteristics of the previous. What it doesn't show is how this originated. magnan

Jehu, Please tell me what anything in your last posts have to do with any of the comments I have made. I don't see any relevance. You are pointing to some problems with universal common descent and I am saying that is different from common descent. I do not think the data supports a tree of life. For the last 550 million years since the Cambrian Explosion the fossil data suggests something else, maybe a lot of bushes but definitely not a TOL. Darwin started the TOL and if it is abandoned then they might give the image that they are abandoning Darwin. However, the data for a common ancestor for "some" species is compelling. Notice I use the word "some." Also nothing is implied about the mechanism for common descent, only that it probably happened. Doolittle is just one more in the long line of scientists who want a naturalistic view of life but apparently does not support a gradualistic one. This list grows but they are not friends of ID. jerry

Here is another quote that may be more illustrative of what I am talking about: A similar inability of still larger datasets to resolve cladogenetic patterns is observed among metazoan clades that diverged even farther back in time. Many recent studies have reported support for many alternative conflicting phylogenies. Jehu

That is a hypothesis that could be tested. From what I understand the similarities are in humans, chimps and other primates; cows, goats and other similar animals. These are only two I know about but I believe there are others.

It has been tested and found to be the case. Read the article Bushes in the Tree of Life. In case you don't understand, not the following quote from the article. "How can it be that despite the availability of large amounts of data and powerful statistical techniques, evolutionary trees upon which experts agree have not been reached? ... We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge. The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics. " Jehu

"But what happens when the pattern of similarities cannot be resolved into a tree because they form contradicting alterantive trees?" That is a hypothesis that could be tested. From what I understand the similarities are in humans, chimps and other primates; cows, goats and other similar animals. These are only two I know about but I believe there are others. jerry

The similarities are very specific and unusual nucleotide sequences.

But happens when the pattern of similarities cannot be resolved into a tree because they form contradicting alterantive trees? Jehu

Come on, people, let’s grow up

I think that's a bit much to ask of PZ. scordova

Common descent and universal common descent are different concepts. Common descent is just the conclusion that certain species have unusual specific similarities with each other that could not happen by chance and is best explained by having a common ancestor. The similarities are very specific and unusual nucleotide sequences. No mechanism is implied but Darwinists assume it is gradualism. These conclusions do not necessarily lead to the proposition that all living things are descended from one or a small number of single celled organisms which is what universal common descent means. jerry

Doolittle also reviewed this articleo n PLoS Bushes in the Tree of Life by Sean Carroll and Antonis Rokas. The article explains that the more genomic data they analyze the harder it is to resolve a tree at all taxonomic levels. Instead, they are left with multiple alternative trees. Everybody here who thinks that commond descent is such a lock should think about these articles. I have argued that what the evidence shows is nested hierarchy that does not resolve into a tree except maybe at the species level. Jehu