Uncommon Descent Serving The Intelligent Design Community

Jerry Coyne: Reason people question neo-Darwinism is that it “is largely consolidated, and is correct”

arroba Email

“Ambition” or “boredom” are behind all the criticism from so many different quarters.

Further to Epigenetics: Dawkins’ “selfish gene” discredited by still more scientists you should have heard of, it seems that Jerry “Why Evolution Is True” Coyne has also noticed David Dobbs’s “Die, Selfish Gene, Die” in Aeon :

I’m constantly puzzled these days by how often people argue that the neo-Darwinian synthesis is wrong, and that we need a new paradigm. Genetic assimilation, epigenetics, horizontal gene transfer—all of these buzzwords are evoked as reasons to jettison our “conventional” view of evolution. But always, when you look at the data, the evidence that these phenomena will overturn neo-Darwinism is nonexistent.

I’ve already written a lot on the epigenetics hype, and have shown that there’s no evidence that a single adaptation in nature involves the fixation in the DNA of an epigenetic alteration of the genome that isn’t initially inherited. Yet people keep banging on about epigenetics.

I’m not sure why the hype continues, but perhaps it has to do with the fact that the main paradigm of evolution—the neo-Darwinian synthesis—is largely consolidated, and is correct. Sure, there are surprises to come, and interesting new phenomena, but there’s no “quantum mechanics” of evolution on the horizon. Some theories don’t need to be overthrown because they’re generally right. Perhaps people don’t like working in a field where there’s no new “paradigm” to forge, and Kuhn has ruined us all!

The “neo-Darwinism is dead” trend may have to do with ambition, or perhaps with boredom. I don’t know. What I do know is that the many recent challenges to neo-Darwinism have all failed to hold water, but people keep pouring liquid into that sieve.

wd400, You simply have no evidence, to support your unsubstantiated claims, that the 'bottom up' materialistic processes of neo-Darwinism can generate radically new body plans:
Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/
Verse and Music:
Psalm 139:15 My frame was not hidden from thee, When I was made in secret, And curiously wrought in the lowest parts of the earth. Oh Come, Emmanuel - Lindsey Stirling & Kuha'o Case - video http://www.youtube.com/watch?v=ozVmO5LHJ2k
wd400, you claim:
Talbot’s questions have been answered (genes also control the spatial and temporal patterns by which other genes are expressed).
Yet, the inability of body plans to be reduced directly to the DNA code is clearly shown by Cortical Inheritance.
Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video http://www.metacafe.com/watch/4187488
Moreover, there are other lines of evidence clearly indicating that the genetic reductionism model (modern synthesis) of neo-Darwinism is false:
In Embryo Development, Non-DNA Information Is at Least as Important as DNA - Jonathan Wells - May 2012 Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns. http://www.evolutionnews.org/2012/05/in_embryo_devel060031.html “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340 “The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences http://musicoflife.co.uk/
As well this piece of evidence:
Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html
This is crushing for neo-Darwinism (genetic reductionism) because these 'Embryonic Electric Fields' presage the morphological development of an embryo:
An Electric Face: A Rendering Worth a Thousand Falsifications - September 2011 Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” https://www.youtube.com/watch?v=wi1Qn306IUU ,,,a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, "When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,",,, I would never have predicted anything like it. It's a jaw dropper.",,,
In fact, not only does 'form' presage morphological development, but 'form' also dictates how the developing cells are used even if there is perturbation to the developing cells of an embryo:
What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. http://www.netfuture.org/2012/May1012_184.html#2
To reiterate,
It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
wd400, So genes control the (epigenetic) system that controls the genes? - - - - This is my last try to explain the Drad enigma, because I'm pretty sure you are pulling my leg: - the genome is shattered in hundreds of tiny fragments - proteins can stitch fragments back together - the mystery is how do the proteins know the correct sequence. How do the proteins know how to align the hundreds of tine DNA fragments in the correct order before initiating repair? - In order to align the overlapping genomic fragments in the correct sequence, proteins (or something) must have knowledge of the correct DNA sequence. - Drad carries DNA copies, however also all the copies are shattered. - So the question is: where does the information (of the correct sequence of the DNA code) reside? Box
Talbot's questions have been answered (genes also control the spatial and temporal patterns by which other genes are expressed). I'm not pretending to misunderstand anything. I see nothing in reconstruction of broken chromosomes by D. radiodurans that challenges the idea sequence information doesn't pass from protein to nucleic acid. If you do you'll have to make you argument much clearer that just pointing to the fact this species and fix double-strand breaks very well. wd400
wd400 #21, Talbott has some questions for you in post #3. I have asked you before if you have any answers. wd400 #22, Surely you are mistaken. Your 'pretending not to understand things' does not impress me at all. I have an email correspondence with one of the researchers who told me that the question of how the hundreds of overlapping genomic fragments are reordered in the correct sequence is "(...) exactly the biggest remaining mystery." Box
Oh, and the "sequence information" in Deinococcus radiodurans is stored in the sequences, even the smashed up ones. That's why homologous recombination, an not-at-all mysterious process, can rebuild them. wd400
Epigenetics means that DNA is being controlled by external forces. But those external forces are in turn controlled by genes. Enchancers are genes, transcription factors are encoded by genes, DNA methylation is maintained by methyl-transferases that are encoded by genes, simiplary histone modifications are down to HDACs which are encoded by genes. Of course genes interact with their environment, including other genes, that's the basis of quantative genetics which is now more than 100 years old. It's still genes that are making proteins (and functional RNAs) that interact with each other and the environment to make organisms. I know lots of people jump on epigenetics as a paradigm-smashing, game-changing blah blah blah. Just not usually people that have any knowledge of the history of molecular biology. wd400
WD400 #18: Same way most organisms repair double strand breaks: homologous recombination. The sequence moves from nucleic acid to nucleic acid, just like mitosis
You didn't answer my question:"Where is this ‘sequence information’ stored – while the genome is shattered into hundreds of fragments?" It doesn't help to refer to analogous processes which are also mysterious. Box
Wd400 #13, I asked you to check your post #13 because it looks like you are informing me about epigenetics?? Which is ludicrous because I’m the one arguing for epigenetics! Last try: ‘DNA as First Cause’, ‘genocentric’, ‘gene-centered’ etc all mean the same thing: DNA is in command-control. Epigenetics means that DNA is being controlled by external forces: DNA is NOT in command-control. See? I was arguing that development and chimerism, with DNA in command-control position – without epigenetics(!), is a mystery. Now it is clear? Box
Same way most organisms repair double strand breaks: homologous recombination. The sequence moves from nucleic acid to nucleic acid, just like mitosis wd400
…. reassembled by proteins, which are encoded for by genes. What’s the problem?
How is Drad's genome reassembled in the correct sequence? Where is this 'sequence information' stored - while the genome is shattered into hundreds of fragments? Box
.... reassembled by proteins, which are encoded for by genes. What's the problem? My comment 13 is what I meant to say too. wd400
While I'm at it: Deinococcus radiodurans, here and here (PDF) - another deathblow to any genocentric (gene-centered) concept of the organism. The genome of the bacterium Deinococcus radiodurans gets reassembled after being shattered by high-dose radiation. Excerpt:
Ionizing radiation can damage DNA in various ways, perhaps worst of all by causing double-strand breaks. These are breaks across both strands of the DNA double helix. The familiar bacterium, E.coli,not at all untypically, dies when it suffers about four double-strand breaks per each of its four-to-eight circular DNA molecules. Deinococcus radiodurans,by contrast, can survive over a thousand double-strand breaks. This means that it continues life after its genome is broken into hundreds of small fragments. It does so by proceeding to put its genome back together again when living conditions improve — a daunting task, to say the least.
wd400, please check your post #13. Something must have gone wrong. Box
... in 1972. We know quite a lot more about the control of gene expression now. It's been a major topic in molecular biology since the 70s, enhancers transcription factors, DNA methylation, histone modification all help to turn unchanging genes into dynamic organisms. wd400
wd400, In post #3 I quote Talbott, who does an excellent job explaining the problem of development with DNA in command. Talbott poses some crucial questions. Do you have any answers? To me it seems pretty obvious, that a bottom-up explanation from two sets of DNA increases the mystery by a multitude. Box
I confess I do not get it. If you want to tell me why you think a population of different (but nearly identical genetically) cells would be disastrous for development you'll have to explain yourself - as it's not immediately obvious. wd400
wd400: Development of a zygote is not a complete mystery, and two nearly identical sets of DNA are unlikely to make it much harder.
You don't see the problem. There was a time that I found it hard to accept that some people just don't get it. However I have come to accept it. Thank you for your candor. Box
Well, that's not the central dogma as Crick (or even Watson) defined it. If you just meant genetic reductionism say that. Devlopment of a zygote is not a complete mystery, and two nearly identical sets of DNA are unlikely to make it much harder. wd400
wd400, Science historian Evelyn Fox Keller paraphrased the Central Dogma: "DNA makes RNA, RNA makes protein, and proteins make us" (2000, p. 54). But I don't want to quibble with you about this, since we both know what is meant: the doctrine, entailing a command-and-control view of DNA, which leads to a mechanistic understanding of the organism. Look at the Talbott quote (post #3). Development from one zygote is a mystery from the perspective of DNA. Now try to solve this mystery with 2 sets of DNA! Box
Box, It's really up to you to explain first what you think the central dogma is (it's not the view that DNA is a first cause) and secondly why you think chimerism or the control of gene expression is add odds with this version of the so-called dogma wd400
wd400, Chimerism isn't at odds with the view of DNA as a First Cause - gene to trait? Please do explain. Box
The central dogma of molecular biology states that sequence information can't flow from protein to nucleic acid. It has nothing to do with chimerism or control of gene expression ( a topic which has been studied since Crick's time). Even the popular (but incorrect) version of the "dogma", that DNA makes RNA makes Protein isn't at odds with these ideas. wd400
The Central Dogma also fails to explain chimerism. This article by the NYTimes is simply amazing. excerpt:" Everywhere You Look As scientists begin to search for chimeras systematically — rather than waiting for them to turn up in puzzling medical tests — they’re finding them in a remarkably high fraction of people. In 2012, Canadian scientists performed autopsies on the brains of 59 women. They found neurons with Y chromosomes in 63 percent of them. The neurons likely developed from cells originating in their sons." How do different sets of DNA cooperate Jerry? Box
Jerry Coyne: Yet people keep banging on about epigenetics. (…) I’m not sure why the hype continues (…)
You shouldn’t be surprised Jerry, because the Central Dogma doesn’t make sense whatsoever – some people understood this back in 1927.
S.Talbott: Another paradox — perhaps the most decisive one — was recognized and wrestled with (and more often just ignored) going back to the early twentieth century. With few exceptions, every different type of cell in the human body contains the same chromosomes and the same DNA sequence as the original, single-celled zygote . Yet somehow this zygote manages to differentiate into every manner of tissue — liver, skin, muscle, brain, blood, bone, retina . . . If genes determine the form and substance of the organism, how is it that such radically different cellular architectures result from the same genes? What directs genes in their temporally and spatially varying activity so as to produce the intricately sculpted and complexly differentiated form of a human being? And how can this directing agency be governed by the very genes it directs? The developmental biologist F. R. Lillie, remarking in 1927 on the contrast between “genes which remain the same throughout life” and a developmental process that “never stands still from germ to old age”, asserted that “Those who desire to make genetics the basis of physiology of development will have to explain how an unchanging complex can direct the can direct the course of an ordered developmental stream” (Lillie 1927, pp. 367-8).
Whoa. Lets think about this. First I agree ambition easily can be behind criticisms of evolutionism as people always want to overthrow paragigms to get the credit. Sometimes this from evolutionist critics of aspects of evolution. Looking to correct and improve anf hopefully change some concepts within the tent of evolution. Sincere critics but motivation is real in man. However, I say however, if CRITICISM of motivations in scientific investigations is legitmate as mr Coyne says THEN monkey see, monkey do. Creationists historically criticized evolutionists for having other motives behind their unworthy acceptance of evolution. Creationist motives were questioned and still are. We can criticize evolutionists and evolutionism for seeing things not there. Just like Mr Coyne says. If Mr Coyne says there is failure in these critics of evolution , though evolutionists, then why not a general intellectual failure?? Whats the equation here? Seems its those guys are wrong! THATS WHAT WE HAVE BEEN SAYING. Unless we are just ambitious and bored! Robert Byers
Coyne seems destined to be left in the dust with his darwin devotion as science moves on. Blue_Savannah

Leave a Reply