Here.
Another non-Darwin ( = serious) book about evolution.
Note: Eugene Koonin’s non-Darwin evolution book not free on Kindle any more.
Act now to get Shapiro free on Kindle.
Jerry “Why Evolution Is True” Coyne is mad about Shapiro’s book:
I haven’t read it but the priceiis right.
Ah, a noviewer!
Jim Shapiro is heterodox in his views and opposed to much of modern evolutionary theory, so this may be a strange book. Weigh in if you’ve read it.
Looks like Coyne’s trollbox will be working late.
Hat tip: Pos-Darwinista
Awesome! Downloading for free to my Galaxy Tab right now. Thanks for the tip.
Tell your friends. It honestly won’t last forever.
Koonin’s book, once free on Kindle, now costs nearly forty bucks.
‘Jever hear the one about the guy who got his books cheaper?
Be that guy.
Seems to cover much of the same ground as the Koonin book.
Possibly with a different slant. It’s far more technical than Koonin. But here’s a readable snippet:
Another interesting snippet:
More interesting snippets:
Here is another interesting snippet which undermines the entire neo-Darwinian framework:
Thus in one fell swoop Shapiro topples the major cornerstone of the non-teleological ‘randomness’ required to be at the base of the atheistic form of neo-Darwinian reductive materialism!!!
Another interesting snippet:
It cannot be understated how devastating the removal of genetic reductionism is for the atheistic/materialistic model of neo-Darwinism that is still predominately taught in schools with no mention of the severe problems that Dr. Shapiro has made clear!!!!
Some research proposals (one of them sounds like Lenski):
Who needs the book when you can just keep posting snippets!?
Genomes are sophisticated data storage organelles integrated into the cellular and multicellular life cycles of each distinct organism. Thinking about genomes from an informatic perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations.
So far, it seems to me as though James Shapiro is trying to reconcile the overwhelming evidence for design with his a priori commitment to evolution and the first thing to be jettisoned in the process is the idea that natural selection acting upon random mutations can provide any significant, or indeed empirically-supported, explanations for the world we live in.
Depends on what you mean by random mutations. All the processes he describes are natural processes, and all of them are part of mainstream biology.
He suggests research targeted to determine randomness with regard to fitness. He does not say the research has been done. He suggests Lenski-like experiments and seems to predict outcomes quite different from what Behe would expect.
All in all, he is well within the mainstream in that he makes hypotheses and suggests ways of testing them.
For some reason I’m having trouble posting. the responses are not showing up as replies.
I’d like to point out that neither Darwin nor subsequent biologists have ever assumed that point mutations are the only source of variation. The mechanisms discussed in this book all come from mainstream biology.
The book is a review of current knowledge, plus suggestions for research.
Please point out where “natural genetic engineering” is not “mechanistic.” I must have missed it.
Perhaps Sahpiro assumes, like Michael Denton, that the game was set up at creation. I don’t know what he thinks about origins.
But he proposes no interventions and is quite explicit in attributing evolution to natural processes.
Have you read any of the book yet, Petrushka? Shapiro repeatedly points out that a ‘mechanistic’ view of biology is wrong.
Have I read the whole thing. No. I just got it this morning. At the moment I don’t have access to it. I’ve read enough to know that my rather lengthy excerpts are representative of his thinking.
I see arguments that some variation is algorithmic in the sense that certain events may be triggered by environmental stress, and some kinds of change may have a statistically better than random chance of being useful. Environmental triggers are mainstream. The non-random nature of changes is not mainstream, but he proposes specific, targeted research to settle the issue.
I also see suggestions for research to verify these conjectures.
I don’t see any invocation of intervention or of non-naturalistic events or processes. I think he rather handily disposes of certain kinds of assertions.
1. He dismisses any challenge to common descent (Microbes are a special case, because they exchange genetic material.)
2. He invokes no intervention, even for the invention of complex functions.
3. He describes a naturalistic process for speciation and invention of new body plans. It’s pretty mainstream: gene or whole genome duplication followed by evolution of the duplicated genetic material.
5. He does not see the Cambrian explosion as an unexpected event.
6. He asserts that mammals share nearly all of their protein genes, and that most of the differences lie in developmental pathways.
7. All of his mechanisms are known and supported in mainstream biology. Feel free to find one that doesn’t come directly from mainstream biology.
So what he proposes — and it’s not entirely new — is evolvability. A concept that has been tossed around for decades. He has an extreme interpretation. I do not intend “extreme” as a pejorative, just a description.
Perhaps we are having trouble with different readings of the term “mechanistic.”
Shapiro contrast it with “informational.”
I find that distinction unfortunate. Computers are machines that process information. They are entirely mechanistic.
If cells can modify their genome in response to environmental stress, it’s still a mechanism. This books suggests but does not produce evidence, that the change mechanism has foresight. He proposes research to demonstrate this.
That’s all good stuff. Conjectures that can be tested.
Yeah, read the whole book first and then get back to us.
Petrushka states at September 27, 2011 at 8:59 am in response to the devastating critique of the genetic reductionism model of the modern synthesis that Dr. Shapiro levels,
Yet in this other thread at September 26, 2011 at 6:08 pm, Petrushka, without reference, hinted at no such trouble for the modern synthesis of neo-Darwinism:
Petrushka is corrected, with several references, here, at September 26, 2011 at 7:35 pm, that observation, nor the modern synthesis of population genetics, offers any support, whatsoever, for his claim that proteins and/or genes can arise by random point mutations!
Petrushka does not respond to this cited refutation; yet just this morning, at September 27, 2011 at 6:29 am, he again, without reference, falsely asserts:
So, shortly after that this morning, when Petrushka states, at September 27, 2011 at 8:59 am, that;,,,
,,,One if left to wonder if Petrushka is even paying attention to the many lies and rationalizations that he repeats over and over, or if he is merely a Darwinbot programmed to spew the same refuted garbage over and over not caring that he has contradicted himself:?!?!
I would also like to point out that even though atheistic neo-Darwinists would very much love to get away from the whole genetic reductionism/point mutation gambit, since it is such a complete failure for them as far as actual empirical evidence is concerned, they are inextricably wed to the scenario to explain the origination of the novel sequences in novel genes and/or proteins. Moreover I would like to point out that whatever relief for finding a alternate source of ‘random’ variation, from the many epigenetic mechanisms listed by Dr. Shapiro, was recently been dealt a severe blow by this following study:
notes
If epigenetic changes aren’t very important for long-term evolution, how does epigenetics falsify evolution?
I don’t see that Shapiro’s book falsifies anything. He asserts that organisms can respond to environmental stress by producing various kinds of genomic changes, and he asserts that some are not random with respect to fitness, but he doesn’t offer proof. He offers some ideas for research.
The word mutation includes point mutations and other kinds of changes. there are at least 20 kinds of changes.
I’m really confused by your assertion that materialism has been devastated. I’d like to see a reference to anything in Shapiro that asserts that the algorithms he sees in cellular machinery are carried out by anything other than physical processes.
Just because a machine executes algorithms doesn’t mean it isn’t physical. Computers do it.
Petruska, please feel free to cite, with actual references, the origination of any novel gene/protein by purely neo-Darwinian (i.e. random material) processes using whatever source of ‘purely random’ variation, epigenetic or point mutations, that you care to postulate.,,, Moreover, I did not state ‘falsify evolution’, I said it was ‘devastating’ to the genetic reductionism model of the modern synthesis of neo-Darwinism!!,,, But if you are interested a actuall Falsification for the reductive materialistic framework of neo-Darwinism, then that is achieved by the following method:
Quantum entanglement is shown to be related to ‘functional information’ by the following evidence;
And yet Quantum Entanglement/Information, which falsified ‘local realism (reductive materialism), is found to be intertwined in the molecular basis life on a massive scale:
Indeed the ‘computation’ accomplished by the non-local quantum entanglement/information within DNA is very impressive:
Anton Zeilinger?, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
And quantum teleporation showed that atoms, which are suppose to be the basis from which functional information ‘emerges’, in the neo-Darwinian framework, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms are suppose to be the basis of!
Petrushka please tell me how quantum information/entanglement can ‘emerge’ from any material basis of atoms when atoms are now shown to reduce to a transcendent basis of quantum information in the first place? i.e. It is IMPOSSIBLE for the ’cause’ for functional quantum information to reside in material particles!!!
Moreover, as you well know Petruska, the dispute between IDists and Darwinists has, thus far, not focused on quantum information so much, if at all, but has instead focused on ‘classical information’,
Yet, though the dispute between Darwinists and IDist has been over ‘classical information,, classical information is shown to be a subset of quantum information by the following method:
And transcendent quantum information is shown, empirically, to be ‘conserved’ here:
I would like to reiterate just how ‘spooky’, to use Einstein’s word, it is to find something that blatantly defies our concepts of time and space, on a massive scale, within our bodies
Further note:
verse and music:
Since this thread is about Shapiro, I’ll quote him:
Petrushka, well by-golly just use a ‘engineered process’, call it natural, (as if that question does not beg the question of where this ‘natural’ engineering process came from all day long), and then claim that these ‘natural engineered processes’ where proteins are custom made for very specific molecular needs in the cell, by the unmatched, extremely sophisticated, intensively parallel, distributed programming of the cell, then claim that this jaw-dropping feat, of manufacturing exactly correct proteins on the fly, is a completely ‘random’ event, that somehow arose by completely random ‘material’ processes, and WA LA, that somehow explains the ‘random’ evolution of exactly the correct amino acid sequences for proteins out of astronomical possibilities?????? Excuse me please!!!,, By chance, is the world you live in down a rabbit hole somewhere?
Perhaps you would like to come back to reality and actually demonstrate that ANY protein can be had by a purely random material processes instead of severely begging the question by appealing to the ‘natural engineering’ of the cell. After you have done that you can work on refuting A.Aspect, and company’s, falsification of local realism and the finding of non-local quantum information in molecular biology!! But then again that would require you being honest with the evidence, so I guess I can count that out!!!
This thread is about Shapiro’s book, so I’ll limit myself to summarizing what hes says.
If anyone thinks I’ve misquoted or misrepresented him him, I’ll respond.
My summary of the relevant points is found at 2.1.1.1.1
What he says about protein evolution is:
He neither asks nor answers where the ability comes from, but the does note that after genome duplication, the duplicate genes are free to change without damaging the organism. He does not invoke any outside agency.
It sounds pretty materialistic to me. Feel free to examine the book and tell me where he appeals to intervention.
There’s one other weird thing about the book. I’ve searched through the whole thing without finding any reference to information loss during mutation.
What I did find is this:
The exact mechanism by which information is conveyed to the genome is controversial, to say the least, but the fact that it happens is something evolutionist have been saying for a long time. Elizabeth Liddle has repeated it over and over in the last month or so.
But there is no controversy about the fact that Shapiro disagrees with those who claim evolution can’t produce information gain. He just thinks genomes learn in much the same way brains learn. I believe he even invokes consciousness.
a few notes:
And it gets better:
i.e. It’s very well likely that ‘natural genetic engineering’, completely by random accident of course 🙂 , stumbled upon functional proteins, out of astronomically large numbers of non-functional protein sequences, that are uniquely tailored for each person; i.e. each human being is very likely to have fairly unique protein sequences, that were ‘naturally engineered’ on the fly, that no one else, or living thing, possesses!!!
How astonishing is that???
further note:
He compares it to the operation of the immune system, which rather quickly finds antibodies through such a process.
If you think it isn’t possible, you should write to him. I’m just reporting what he says.
Petrushka, Well actually there is no hint of such a highly choreographed ‘search and find’ mechanism, as employed in the immune system, for making proteins i.e. the proteins hit the target first time, every time, to sequence dictated by ‘natural genetic engineering’, or else they are immediately destroyed by the ever finicky ribosomes;
Whereas searching for correct novel functional protein sequences, out of astronomical amounts of non-functional protein sequences, would look much more akin to this:
,,,which, regardless of the neo-Darwinists severe distortion of the immune system for propaganda purposes, to ‘sell the lie’ of neo-Darwinism, the fact is that the immune system still severely begs the question, because the immune system is in fact another stunningly elegant example of Intelligent Design:
In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparative Immunology, where he realized that the papers published were comparative studies that had nothing to do with evolution at all.
note:
As well, the ‘protein factory’ of the ribosome, which is, as far as I know, the only machine in the universe capable of making proteins, is far more complicated than first thought:
Music:
Perhaps this song is more fitting for the ‘perfectionist’ ability of ribosomes to hit the bullseye:
I think your disagreement is with Shapiro, not with me.
Petrushka, since you seem to agree that Shapiro is wrong also, as I do, when you state;,,,
,,,Please point out the unfounded presumptions in the statement you cited.
Test
My comment 6.1.2.2, which is a quote from the book, and your response, 6.1.2.2.1, in which you argue with me, rather than with Shapiro.
Throughout this thread I have done little else but cite quotations from the book. At several points I have characterized his understanding as mainstream and have praised him for outlining lines of research to support his conjectures.
I do find this statement to be oddly worded.
I would characterize evolution as an effective search, but if it doesn’t know future needs, it is blind. I think what he is saying is that evolution has an effective way of generating variations, not that it knows in advance which variants will prove useful.