Michael Denton’s new book is out, Evolution: Still A Theory In Crisis.
Denton’s stance is for structuralism and against functionalism, especially as functionalism appears in it’s current form as the modern synthesis or neo-Darwinism (the cumulative selection of small adaptive changes).
Denton argues for the reality of the types, that “there are unique taxon-defining novelties not led up to gradually from some antecedent form” and that the lack of intermediates undermines the Darwinian account of evolution. He also argues that a great deal of organic order appears to be non-adaptive, including “a great number of the taxa-defining Bauplans,” and that this also undermines the Darwinian account of evolution. Evo-devo is also showing us that “Darwinian selection is not the only or even the main factor that determined the shape and main branches of the great tree of life.”
These arguments are first set forth in Chapters 3 through 5 of the book and then defended throughout the subsequent chapters.
Denton provides a list of some of the Type-Defining Homologs:
The Pentadactyl Limb
The Feather
The Insect Body Plan
The Flower
The Amniotic Membrane
It is not just the major taxa which are characterized by unique defining homologs or novelties:
Centipedes
Beetles
Ants
Butterflies
Even individual species are often defined by unique novelties (autapomorphies in cladist terminology).
To head off a lot of irrelevant objections and nonsense from people who can’t be bothered to read the book, Denton accepts common descent and doesn’t appeal to “goddidit” as a better explanation.
- If types exist, what does that mean for Darwinian evolution?
- Does the existence of non-adaptive order undermine Darwinism?
- Does anyone think neo-Darwinism is even relevant to modern evolutionary theory?
I should add, I think there is less reason in this day and age to resort to protein phylogenies and Dayhoof diagrams because we can now go to the genes themselves.
The story is far clearer in the gene of the Cythochrome-C than then protein because the Cytochrome-C is implemented with different intron patterns (no spliceseosomal introns in bacteria, for example).
As Dave Carlson pointed out, there is only limited information in the Dayhoff diagram to draw conclusions from.
What do you mean by a species in prokaryotes? I ask because my understanding is the designation is somewhat arbitrary.
Good question. It does relate to the OP where Denton argues there are discrete forms rather than a continuum.
FWIW, that typological perception by Denton is why I remain a creationist. Granted we can build that nice looking protein Dayhoff diagram that seems to just scream common descent, but it’s the isolated diagnostic characters (what I call Taxonomically Restricted Features) that don’t look like there was a smooth transition from one major group (like prokaryotes) to another (like eukaryotes).
Are there discrete entitites in the prokaryotic world enough to define species? Can’t say for sure, but…
Tthere do seem to be discrete architectures as discussed by Shapiro and Sternberg:
http://shapiro.bsd.uchicago.edu/Shapiro&Sternberg.2005.BiolRevs.pdf
Hey, look at that, Richard von Sternberg (the star of one of the YEC Baraminology conferences) is in league with James Shapiro! Whoa!
Sternberg is a process structuralist which I read to mean, he doesn’t involve himself in the big philosphical origins issues. Shapiro thinks bacteria can re-engineer themselves sufficiently.
But it’s stuff like this, like what Shapiro and Sternberg said in the above paragraphs, that keeps me on the non-UCA side of the aisle.
Nothing personal to those who disagree at TSZ, I just can’t reconcile the idea of UCA with these Taxonomically Restricted Features — they look too much like a poof out of nowhere.
Slight changes to mtDNA and building MRCAs for species, I can buy that and I have no argument using phylogenetic methods on species that center around the same Taxonomically Restricted Architectures.
stcordova,
Because there wasn’t. Endosymbiosis is a rare exception to Darwin’s supposition of gradual, incremental change. Still evolutionary, though. Unless you know different.
stcordova,
So, if evolution were true, you would expect every feature to be present in every organism? Or history to be preserved in detailed succession?
stcordova,
The MRCA of any given collection of modern asexual organisms is no more ‘the MRCA of the species’ than mitochondrial Eve’s mitochondrion was the first mitochondrion ***. Mitochondria are effectively prokaryotes living in intimate association with our cells.
*** [eta – badly expressed: that first cell is the ‘MRCA of the species’ if ‘the species’ is considered to be the current collection one is looking back from. But it would be a mistake to infer that this is the first instance of a member of that species.]
A classic.
So are you saying that there could have been tens of thousands of members of the species in the population at the time of this MRCA (pick Eve, or Bob, or Larry, etc.), but the descendants (or lines of descent) of all but the MRCA either died out or interbred with descendants of the MRCA?
Flint,
Well, my comment was specifically about asexual non-recombining lines. But yeah, basically. It is an inevitable consequence of iterative copying in a finite world (barring frequency dependent effects) that a given copy of a DNA stretch will either leave no descendants in the future, or it will be the only one to do so from a broader collection of alternative instances. There is no need for a bottleneck for this to happen.
Asexuals (and mitochondria and Y chromosomes) are conceptually simpler because the DNA stretch is inherited as a piece. Recombinational events (sex and HGT) slice things up a bit.
Agreed, even from a YEC standpoint. YECs believe the patrilienal MRCA male is not Adam (the first instance) but Noah (a much later instance).
Abraham Modal haplotype aligns with YEC Abraham who is a mere 500 years after YEC Noah.
But Y-chromosomal Adam(Noah) does not align with YEC Noah unless one invokes accelerated Y-chromosome mutation for a burst of 500 years. But there is no good independent reason for invoking accelerated mutation except to make the mainstream Y-chromosomal Adam(Noah) align with YEC Noah. For now it is a thorn in the side of YEC even though Lowe and Shearrer’s mtDNA Eves (human, doggie, cattle) seem to support the YEC narrative with the mtDNA Eves at 10,000 years or less.
Still not, I’m afraid. She is not theMRCA but anMRCA. She’s the MRCA of our mitochondria. Period. Other bits of our genomes have different MRCAs. The article chosen isn’t a semantic quibble but an important difference in the meaning of “MRCA”.
You misunderstand Joe and, apparently, Wiki. Joe and I are in agreement on all of this.
While this is trivially true, your maternal grandmother, e.g., is not the most recent common female ancestor of you, your siblings, and your cousins. Your example breaks down in one generation.
Yes, as I’ve said already. And those are the conditions, as I’ve said also: that reproduction is truly asexual and that there is no selective process (like frequency-dependent selection) promoting preservation of genetic diversity.
stcordova,
Not aware of a study that places Eve much closer than 60,000 years, or Adam less than 120,000, to say nothing of the inconvenient mosaic that forms the rest of the genome.
Domestic animals, I can buy, since there is high inbreeding and strong selection. What would be interesting is if the rest of the Ark followed your hopes. I bet it doesn’t!
Sal,
Can I get the citation(s) for this:
Thanks.
Agree in principle, but not always in practice.
For yeast or bacterial species, where populations are way over trillions and geographically separated, it seem hard to believe one individual genome will fix (overtake) the entire population.
It seems far more reasonable to me there was an allopatric-type split off (or if one is a creationist, a creation event) rather than some fixation of the MRCAs genes to all members of the global population of that species.
Sal, when you provide a citation, please give sufficient information to find the actual paper being cited. “Lowe & Shearrer” is not sufficient.
Seems to be a horsie thing
stcordova,
I don’t see why that’s harder to believe than one or two individuals generating the larger population from scratch.
What seems reasonable to you may not be objectively reasonable. What seems hard to believe to you may not be objectively unlikely. In fact, under neutral theory and/or coalescent theory, a single MRCA (in a strictly clonal species with no selection favoring diversity) is inevitable. It’s just longer ago for larger populations. And again, there is an equilibrium level of standing genetic diversity, given any particular population size. You may think some yeast species has not reached that equilibrium yet if you prefer, but your gut feeling isn’t good evidence. I will also point out that allopatric speciation doesn’t generally involve a bottleneck. You may be thinking of peripatetic or founder event speciation, which are special cases.
If one “species” of bacteria or yeast “takes over” the population, why are there multiple species of bacteria and yeast? Isn’t it simpler to say that one lineage was successful and diverged from other lineages?
Glad to oblige.
Loewe and Scherer actually wrote a review article that was based on lab experiments that clocked the mtDNA mutation rates by sequencing mother and daughter pairs rather than using evolutionary inferences from chimp human divergence. So, imho, it was far more accurate. No one has dared to try again.
In contrast, the deep pedigeree study of the human Y-chromosome agreed with the Chimp human mutation rates.
If you can’t access the article through the pay wall, I may be able to help. Since you’re a university student, I think you can access it through your school’s institutional access like I do.
Here you go:
http://www.ncbi.nlm.nih.gov/pubmed/21238138
Sorry for the earlier misspelling!
petrushka,
Yes, that’s pretty much it. I’m never very comfortable with ‘population thinking’ in prokaryotes. Or ‘species’. They are all ‘strains’.
Well the following is for diploid sexually reproducing species, but I guess the asexual species will have comparable time frames:
If we have a quadrilion individuals and they are geographically dispersed and hence not well stirred, I doubt there will be enough time in the life of the Solar System for there to be overtake in such a population.
At best overtake would happen in a little isolated space (about the size of a petri dish in lenski’s lab) and in the first few thousand generations, after they spread out and billions of generations later, I’d say forget any one individual genome overtaking the population except by super selective global sweep of planet Earth.
DNA_Jock,
that phenomenon is called genetic equidistance. It has been recognized, rightly in my opinion, by Mike Denton as “ , also “one of the most astonishing findings of modern science”. in his 1986 book “Evolution, A Theory in Crisis”.
By all means feel free to post an abstract or a link that works.
The claim appears to be rubbish, based on a 1997 estimate of mutation rate in non-coding DNA, which accumulates mutations ten time faster then the coding regions.
stcordova,
What you quote is about fixation, not coalescence. But yes, coalescence time is, if I recall, about 4N generations for a population of constant size N. I still don’t think this fits whatever point you’re trying to make. But perhaps it isn’t clear to me what point you’re trying to make.
Is this in fact an attempt to justify a worldwide flood about 5000 years ago?
Joe Felsenstein,
Denton on page 28: “I also have omitted discussion of the problem of the equidistance or equal isolation at the molecular and genetic level of the members of specific clades from particular outgroup species. While this fascinating phenomenon is still as challenging as ever to the Darwinian narrative, it has been reviewed in detail by Shi Huang in a number of recent papers. He has shown that the equidistance phenomenon can only be accounted for if the origin of the different Types involved causal factors in addition to cumulative selection and drift and if the origin of the major types was saltational rather than the gradual process described by defenders of Darwinian orthodoxy.74”
The genetic equidistance. has been interpreted by the universal molecular clock hypothesis. However, that has now been proven to be a major and costly mistake. The correct solution is the maximum genetic diversity hypothesis, as explained in this newly published paper of mine on the old riddle of genetic diversity, also a preprint of it here,
That is difficult to believe given this statement of yours in response to the overwhelming evidence that the Noachian flood never occurred:
Are you honestly saying that you’d no longer be a creationist if Denton’s claims were addressed? I suspect that you would not change your beliefs one iota since they serve an emotional need and are not based on evidence.
No-one is arguing that the prokaryote population of earth was eternally steady-state and huge. But equally, it is not the case that the alternative to fixation within such a background is descent from a solitary ancestor. The MRCA of any given collection can easily be a member of a population, which had a prior MRCA.
Joe Felsenstein,
Why then there is still a century old riddle of genetic diversity , if all these scientists are so great?
What the eff is this all about? Bacterial lineages are not species in the same sense as sexually reproducing species. If a “mutant” bacterium survives, it and its lineage will continue diverging. There is no population to replace, unless there is horrific selection pressure. Which is unlikely outside a lab or hospital.
petrushka,
Well yes, selection (really, ecology) changes expectation. You can’t ‘take over’ a niche for which you are not well adapted. So with a range of niches, the neutral assumption can’t hold.
The point I’m trying to make is this:
The best explanation unicellular species may have identical DNA for certain genes is that they came from a recent MRCA. By recent, I mean on the order of a few or several million years, not hundreds of millions of years.
The major splitting off of the lineages could be hundreds of millions of years back, and that is inferred by interspecies comparisons. The MRCA however of a species isn’t usually inferred by interspecies comparisons but INTRA-species comparisons — mtDNA Eve was inferred via INTRA-species comparisons, and the best clocking of the mutation rate was done by INTRA-species comparisons as well, and it yielded a 6,500 year date for mtDNA Eve who is also the matrilineal MRCA of all humans.
I’m going out on a limb and suggesting E. Coli “Eve” (ha!) wasn’t that far back. What would MRCA be for all the other unicellular species.
Is there an E.coli Adam?
When the ancestor to E.coli fissioned, was one product a different species?
Exactly! 🙂
That’s why I think E. Coli has an MRCA that’s not that far back. I’m posting here to get some idea of what methodology can be used try to find out when E. Coli or any unicellular species were founded by their MRCA.
The phylogenists are obsessed with when lineages split, but I’m interested in the MRCAs which may not correspond to some of the major splitting times.
I went out on a limb and said most MRCAs of species will not be that far back (several million years at most, not hundreds of millions of years).
This all relates somewhat to the OP and Denton’s view of types and discrete forms and plans. Each of these forms will have an MRCAs of species to boot. Denton probably doesn’t care about the species MRCAs but the existence of species MRCAs will serve to highlight Denton’s viewpoint.
If we have all the species level MRCAs recent but the supposed ancestral splits millions of years back, that would be consistent with the Orchard model rather than the Universal Tree of Life and provide indirect support to Denton’s view:
So instead of Taxonomically Restricted Features, how about I use the term automorphies to define species. Yeah, automorphies!
What was the first E.coli before it was E.coli?
stcordova,
That’s not all that far out on a limb, to be honest. I would tend to agree, if we are careful about what we mean by ‘species’. Most species will have a MRCA of the order of a few thousand to a few hundred thousand years ago. That means, of course, the most recent individual that figures in every family tree, not the originator of the species.
Huh? But how can the earth/cosmos also be young?
This argument is on the other side of the looking glass.
I think, Sal, you may be forgetting that an MRCA, in a recombinational scenario, refers to one segment of the mosaic genome only, not the whole thing. Each DNA base has a notional MRCA. For neighbouring bases, they tend to coalesce on the same individual. But the entire mosaic of our genome has many MRCAs, living at different times.
Equally, one can be a MRCA and contribute NO bases to the future population – only ‘descendants’.
Somehow, I think all this is being lost when it is translated to SalSpeak.
I’m not, as Joe said:
But that’s why I’m asking about unicellular species, not withstanding there is some HGT.
Not withstanding HGT, is it a fair assumption that for asexually reproducing species, there is not a mosaic of DNA from multiple lines of ancestors, but only one line of ancestry that is maybe interrupted by HGT, hence there isn’t a mosaic contribution, just cumulative mutations in the line with some HGT on the way.
The issue of sexually reproducing creatures does seem substantially more complicated, and it was worth the price of admission to this discussion to see that I had weaknesses in the way I understood the issues of MRCA for sexually reproducing species. As Joe so eloquently said:
But you are ignoring the fact the the point of divergence for a strain of bacteria is not the origin of the “species” or type.
Glad to hear it, but if you do appreciate what a sexual MRCA represents, I find this puzzling:
That one individual may be the original possessor of a ‘universal’ 10,000-bp segment of our DNA (and another of another 2,000, etc) does not serve to highlight Denton’s viewpoint IMO. There is nothing special about these individuals nor, necessarily, about the DNA we all inherited from them. They got it from their parents.
stcordova,
Yes, it’s fair. But, like the MRCA of a sexual organism’s DNA stretch, there need be nothing special about the MRCA of that particular linkage unit for it to become, in the fullness of time, a MRCA.
Bring on the M&Ms
Corrections on my part:
contrast with:
and
Apologies to the readers.
…and then you proceed to make no clear point. Seriously, I’m having great trouble figuring out what you’re trying to say. You are not expressing your ideas clearly, partly perhaps because you are unclear on the terminology. Certainly the MRCA of an asexual population will often not be as old as the population, and in fact much, much younger if there has been a selective sweep recently. If two sequences are identical, there are two reasonable explanations: either they share a recent common ancestor or they are under purifying selection.
Your 6500-year estimate for mtEve is not widely accepted. Have you ever read a critique of that paper? If your goal is to fit all the data into a global flood, good luck. There never was any such thing.
stcordova,
Unicellular != asexual. Get that out of your head, at least.
Done!
Purifying selection for the entire genome where nucleotides are treated particulately isn’t feasible ala Kimura.
Sure you can fix the traits of one individual by wiping out the rest of the population because that individual had the trait that kept it alive, but it doesn’t mean purifying selection was in play for the other traits in the genome.
This scenario is effectively a bottle neck.
So MRCA is good explanation if we are talking no mosaic of mutiple ancestral lines, but only one ancestral lines (with some HGT).
But there is something I didn’t mention, that is more important. What if we find there are really no creatures that have far back MRCAs. What if the living fossils like horse shoe crabs from different geographic regions, sharks, nautilus maybe plants. What if we find samples form widely separated geographical contexts and the MRCA is recent?
This would be an interesting test of the hypothesis:
http://geology.about.com/od/fossilstimeevolution/qt/livingfossilplants.htm