Surprise, Human Genome Didn’t Solve All the Mysteries: Life is Complicated and Evolution Fails Yet Again

_{Cornelius Hunter
July 10, 2011

Intelligent Design

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Intelligent Design}

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Here is a Nature News Feature that speaks volumes about the state of evolutionary theory. It explains how the Human Genome project and high throughput technologies have revealed levels of complexity evolutionists hadn’t even dreamed of. It is yet another monumental failure of evolutionary theory, even though we all know evolution is a fact. Read more

Comments

So how is it you can claim that a bifurcating nested pattern is a prediction of Darwinian theory? Or has that prediction been falsified?Mung_{July 14, 2011
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Much more bushy. Cloning organisms don't speciate, by definition.Elizabeth Liddle_{July 14, 2011
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Extant and fossil species can be readily placed on a bifurcating tree.
All life, or only some of it? What does that tree look like for single celled organisms?Mung_{July 13, 2011
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OK, here are my reasons for accepting common descent as likely: Extant and fossil species can be readily placed on a bifurcating tree. This tree is supported by two independent lines of evidence: phenotypic and genetic. We understand a lot about the kind of mechanisms of inheritance, and the generation of variation that account for individual differences. We know that heritable differences in reproductive efficiency exist, and are a function of the current environment. This gives us a mechanism by which both evolution over time within a population, and speciation (the divergence of a population into to independently adapting populations) can occur. We see this mechanism operating in the lab, field, and in computational models and applications. It predicts extinct species at specific eras whose fossils have subsequently been found. What's not to like? See you tomorrow :) LizzieElizabeth Liddle_{July 12, 2011
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However if you go to Amazon and type it in you’ll find several weighty tomes that seem suitable. I can link to them if you insist,
Please. I type in common descent or common ancestry and get things completely unrelated. Maybe I should try descent with modification.
...but what’s your point?
My point is that I'd really like to find a good book that even tries to make the case. I have no idea why people believe in this theory. And I'd like to know why. I can't even find a good book on it.Mung_{July 12, 2011
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Mung:
Hi Liz, Thanks for the link. So there isn’t just one single gene for beak size. That’s the way I read it. Agreed?
Looks like it. And I'd expect there to be more than those they found.Elizabeth Liddle_{July 12, 2011
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Mung,
I want you to give me the name of a really good book on common descent. One that sets out the arguments and evidence. Up to the challenge?
Are you up for the challenge of providing the same for Intelligent Design? Specifically the evidence aspect? As to good books on common descent specifically, well I can't recommend anything on that single topic alone. However if you go to Amazon and type it in you'll find several weighty tomes that seem suitable. I can link to them if you insist, but what's your point? You can refute every page in every such book? I hardly think so. That you find them unpersuasive is of little actual consequence. Publish or perish!WilliamRoache_{July 12, 2011
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WilliamRoache:
Crack a book.
Sure. Always willing to do that. I want you to give me the name of a really good book on common descent. One that sets out the arguments and evidence. Up to the challenge?Mung_{July 12, 2011
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Hi Liz, Thanks for the link. So there isn't just one single gene for beak size. That's the way I read it. Agreed?Mung_{July 12, 2011
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A: Crack a book.
Like these? Lewin Watson Though my copies may be a bit dated by now. Hard to stay current with textbook costs as they are.Mung_{July 12, 2011
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Article here on the genetic followup to the Grants' original work: http://www.hras.org/sw/swjan07.htmlElizabeth Liddle_{July 12, 2011
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Mung,
How do you measure a gene?
A: Crack a book.WilliamRoache_{July 12, 2011
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PaV:
This quote caught my eye: “When we started out, the idea was that signalling pathways were fairly simple and linear,” says Tony Pawson, a cell biologist at the University of Toronto in Ontario. “Now, we appreciate that the signalling information in cells is organized through networks of information rather than simple discrete pathways. It’s infinitely more complex.” IOW, “signalling information” is “infinitely complex”. And all of this was brought about by RM + NS! Wow! RS + NS is God-like!! It can do “infinite” work!!!
Well, yes, it probably can (well, not infinite, but it might as well be). That's the thing about non-linear systems - a simple algorithm can result in infinitely complex structures and patterns.
Elizabeth Liddle: You ask what the relevancy is here. It is this: Darwin wrote a book in 1859. It wasn’t science. It was a ‘theory’ about the science categorized as ‘biology’. But this theory was incorporated into science, and plays the prominent role in trying to understand the science of biology. In 2008, Stephen Meyer wrote a book. It wasn’t science. It was a ‘theory’ about the science called ‘biology’. The question now is: will this ‘theory’ (Intelligent Design) be incorporated, or not, into the science of biology? You’ll note that in the linked article ‘systems biologists’ are at a crossroads as to how, what, and where to explore the genome. Having the wrong understanding of biology (Darwinism) can be incredibly costly, leading to many dead-ends, representing a tremendous loss of time, energy and resources. All of this is not a matter of indifference.
Well, having a wrong understanding of science can be very costly, and lead to dead ends, but I'm not seeing Darwinism as the problem here. Nor am I, in fact, seeing a dead end. On the contrary, I'm seeing a huge opening out of opportunities.
Here’s another quote: “The fundamental idea that the genomic regulatory system underlies all the events of development of the body plan, and that changes in it probably underlie the evolution of body plans, is a basic principle of biology that we didn’t have before,” says Davidson.” So, “changes in [the genomic regulatory system] probably underlie the evolution of body plans is a basic principle of biology . . .
Yes, it probably is. People do tend to ignore development, or have done up till now. As a developmentalist I welcome ~~our new developmental overlords~~ this new emphasis on development.
Well, now, exactly how does Darwinism explain the fact that ‘body plans’ arose in the Cambrian, 550 mya, and haven’t arisen ever since?
Well, it depends what you mean by body plans. Lots of new body plans have arisen since (and don't forget flora), but certainly bilateria got off to a pretty good start. Once you have a successful lineage, the chances that its successors will dominate subsequent global populations becomes high, and the genes that specify it (what we now know as hox genes) will be highly conserved.
I can so no manner in which Darwinism can even attempt such an answer. (I’m, of course, assuming one approaches this with intellectual honesty!)
I appreciate your assumption :)Elizabeth Liddle_{July 12, 2011
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btw: I do enjoy talking to you, Mung :) Your questions are very refreshing.Elizabeth Liddle_{July 12, 2011
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Mung:
How do you measure a gene?
Well, you sequence it - figure out what the DNA sequence is.
How do you measure the frequency of a gene in a population?
Presumably you mean an allele - you sample from the population, and count the alleles in your sample.
How do you know that changes in mean size of finch beaks was caused by changes in gene frequencies?
The Grants didn't do genetics, they were working with phenotypes. But the genes have been studied subsequently. I'll try to dig out the papers. IIRC there was variance in a gene that controlled the developmental time table of gene expression in beaks.
Which gene or genes were being measured?
I'll look that up.Elizabeth Liddle_{July 12, 2011
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How do you measure a gene? How do you measure the frequency of a gene in a population? How do you know that changes in mean size of finch beaks was caused by changes in gene frequencies? Which gene or genes were being measured?Mung_{July 12, 2011
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Yes indeed. We always need something to measure. Alleles are reasonably easy to measure. Gene is still a useful concept. But as we know know, what we inherit from our parents is not confined to genes.Elizabeth Liddle_{July 12, 2011
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There needs to be an IT for IT to increase in frequency in the population.Mung_{July 12, 2011
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Most terms coined originally to denote a category find themselves with a region instead. More things in the universe are continuous than discrete, which is why quantum mechanics remains a bit surprising. So the word "gene" may have had its day in the sun. I hope so, actually, But that doesn't mean that it won't remain a reasonable workhorse concept in heritability.Elizabeth Liddle_{July 12, 2011
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Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements... What is a 'gene' nowadays? James Shapiro won't even use the term anymore without [putting quote marks around it.Mung_{July 12, 2011
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Declaring simplicity as an evolutionary prediction puzzles me. When the human genome project started, most scientists were betting on 100K+ protein coding genes. The sparcity was a bit shocking. Then miRNAs, complex regulation, etc., started to make things look a bit more complex. But complexity as a failure of evolution? Odd.DrREC_{July 11, 2011
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This quote caught my eye:
“When we started out, the idea was that signalling pathways were fairly simple and linear,” says Tony Pawson, a cell biologist at the University of Toronto in Ontario. “Now, we appreciate that the signalling information in cells is organized through networks of information rather than simple discrete pathways. It’s infinitely more complex.”
IOW, "signalling information" is "infinitely complex". And all of this was brought about by RM + NS! Wow! RS + NS is God-like!! It can do "infinite" work!!! Elizabeth Liddle: You ask what the relevancy is here. It is this: Darwin wrote a book in 1859. It wasn't science. It was a 'theory' about the science categorized as 'biology'. But this theory was incorporated into science, and plays the prominent role in trying to understand the science of biology. In 2008, Stephen Meyer wrote a book. It wasn't science. It was a 'theory' about the science called 'biology'. The question now is: will this 'theory' (Intelligent Design) be incorporated, or not, into the science of biology? You'll note that in the linked article 'systems biologists' are at a crossroads as to how, what, and where to explore the genome. Having the wrong understanding of biology (Darwinism) can be incredibly costly, leading to many dead-ends, representing a tremendous loss of time, energy and resources. All of this is not a matter of indifference. Here's another quote:
“The fundamental idea that the genomic regulatory system underlies all the events of development of the body plan, and that changes in it probably underlie the evolution of body plans, is a basic principle of biology that we didn’t have before,” says Davidson."
So, "changes in [the genomic regulatory system] probably underlie the evolution of body plans is a basic principle of biology . . . Well, now, exactly how does Darwinism explain the fact that 'body plans' arose in the Cambrian, 550 mya, and haven't arisen ever since? I can so no manner in which Darwinism can even attempt such an answer. (I'm, of course, assuming one approaches this with intellectual honesty!)PaV_{July 11, 2011
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Elizabeth, so in your view if life was found to be relatively simple, as was generally expected, from the neo-Darwinian framework, going into to Human Genome project, then neo-Darwinism would have been vindicated, but alas now that the 'simple' neo-Darwinian expectation has been literally crushed, by the finding of incomprehensible integrated complexity, now this does not hurt Darwinism in the least??? ,,,Ever hear the saying that a theory that explains everything explains nothing??? Elizabeth,,, a few notes as to a few problems you seem to have overlooked in your haste to be a good faithful, cheer-leading, Darwinbot,,, Scientists Map All Mammalian Gene Interactions – August 2010 Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome. http://www.sciencedaily.com/releases/2010/08/100809142044.htm Poly-Functional Complexity equals Poly-Constrained Complexity The primary problem that poly-functional complexity presents for neo-Darwinism, or even Theistic Evolutionists is this: To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained to random mutations by poly-functionality, I will use a puzzle: If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome of say 500 interdependent genes, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their falsified genetic reductionism scenario I might add, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford. S A T O R A R E P O T E N E T O P E R A R O T A S Which is translated ; THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS. This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation. This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations. The puzzle I listed is only poly-functional to 4 elements/25 letters of interdependent complexity, the minimum genome is poly-constrained to approximately 500 elements (genes) at minimum approximation of polyfunctionality. For Darwinist to continue to believe in random mutations to generate the staggering level of complexity we find in life is absurd in the highest order! As to Theistic Evolutionists, who believe God guides evolution incrementally, all I ask you to consider is do you think that it would be easier for God to incrementally change the polyfunctional genome of a organism, maintaining functionality all the time, in a bottom up manner or do you think it would be easier for Him to design each kind of organism in a top down manner? The evidence clearly indicates 'top-down' design. “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.” R. Milner, Encyclopedia of Evolution (1990) Notes: Insight into cells could lead to new approach to medicines Excerpt: Scientists expected to find simple links between individual proteins but were surprised to find that proteins were inter-connected in a complex web. Dr Victor Neduva, of the University of Edinburgh, who took part in the study, said: "Our studies have revealed an intricate network of proteins within cells that is much more complex than we previously thought. http://www.physorg.com/news196402353.html Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information – David L. Abel and Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.htmlbornagain77_{July 11, 2011
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Cornelius Hunter: I honestly don't understand what point you are making with your blog piece. Why does Life being Complicated mean that Evolution Fails Again? What are you you referring to when you talk about when you reference: "Evolution’s simplistic, gene-centric, just-add-water view of biology"? Who does "Evolution" represent in this sentence? Presumably not Darwin, who didn't know about genes and had a vaguely Lamarckian idea of the origin of variation? In fact, presumably not any "Darwinist" who places Darwin's theory of Natural Selection at the centre of evolutionary theory? Maybe Dawkins, but smart cookie though he is, he's not that smart, and there are many who dispute the gene-centred approach of The Selfish Gene, though it is a moderately useful model for some limited purposes. What I find difficult to understand is why anyone should think of the enormously exciting recent discoveries in genetics some kind of Evolution Fail. The really exciting thing, to me, about the availability of GWAS findings is that they make it abundantly clear that most traits are polygeneic, and involve gene-gene interactions and gene-environment interactions. This solves a lot of problems for simplistic natural selection theories (where single alleles had to be greatly advantageous to be selected), because it puts the focus back on the locus of natural selection, namely, the organism, which is where Darwin had it in the first place.Elizabeth Liddle_{July 11, 2011
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Mung:
Finch beaks change in size. There is no known force which can stop the motion of change in finch beak sizes. You must refute Newton to demonstrate otherwise.
Also pelicans. And I don't recommend getting into an argument with a pelican.Elizabeth Liddle_{July 11, 2011
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This quote caught my eye: '"The more we know, the more we realize there is to know." Seems this is a prediction of Theism,,, i.e. a finding truly befitting to the endeavor of studying the handiwork of a infinitely powerful Creator.bornagain77_{July 11, 2011
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Makes one wonder - or should make one wonder - "could pure Biology be done without evolutionary assumptions?" Think about it: if all the current new information we find through biology simply refutes many of the guesses attributed to belief in Darwinian evolution, would it not be more preferable to dispense with such pretensions in order to get at a clearer picture of what's really happening? Does biology require Darwin to guide it? Apparently not.CannuckianYankee_{July 11, 2011
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Finch beaks change in size. There is no known force which can stop the motion of change in finch beak sizes. You must refute Newton to demonstrate otherwise.Mung_{July 10, 2011
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