And an interesting response from ENV. I do want to point out the professional tone, which I appreciate.
From the ENV article:
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Was not sure if I would respond, but this is a good place to start.
First of all, this does not undermine common descent in any way. Interestingly, the article seems to indicate that common descent in whales to terrestrial ancestors is not the target here. Given that that is what we mean by “evolution,” I’m not even sure I have a dog in the fight.
Second, Dr. Jones is correct that it is difficult to simultaneously evolve a pre-specified set of 4 mutations. This is often called the “waiting time” problem. This fact alone, however, tells us nothing about the evolvability of whales. There are a string of conjectures that must all be demonstrated true for the waiting time problem to be a reasonable model of whale evolution. Failing to justify or expose these conjectures is a large modeling / mathematical error. It is for this reason, I would say that the whole argument is in serious error, even though the math behind the waiting time problem is correct (sort of).
Does anyone want to articulate the string of conjectures that must be true for the waiting time problem to apply?
Simply put, there are some things that might be improbable in evolution, but there is no evidence if any improbable steps are required in whale evolution.
The Evolution News article argued that for a land mammal to become a whale, or a Batmobile to become a Yellow Submarine, it would require multiple coordinated changes. To many people this would be a trivial and common sense assumption, even without the detail given in the article.
Except science defies common sense all the time. Biology defies common sense all the time too.
This gets to the core problem. The whole argument is predicated on an unjustified assumption, with which I disagree. It is possible that a specified-set of mutations is required to evolve whales, but Dr. Jones has just assumed this to be true. No evidence is offered. No evidence is found.
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This also turns out to be a very large equivocation.
Moreover, some even turn out to be essential, which would be very odd if they have been added last by evolution. The existence of these genes is a common problem elsewhere in the evolutionary story, even though it appears not to be relevant to whales. Protein coding genes are hard to explain when they appear de novo — see Doug Axe’s work as well as this recent EN article .
Doug Axe’s work is not at all about “protein coding genes,” but about stably folding and complex enzymes. These are very different things (one set is much larger and includes the other), and most (almost all?) “de novo” genes in mammals are of the former variety, not the latter.
This piece of fallacious reasoning is a replay of an earlier analysis that winning the lottery is not just difficult, but virtually impossible, if you calculate odds based on the idea that you not only have to calculate the odds of a single person out 14 million people winning … but you have to calculate the odds of precisely “Joshua Swamidass” winning the lottery!
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On peaceful science I saw where someone posted about the Antarctic basilosaurid at 49 mya. That’s the press release. The paper ended up dating it at 40-46mya which is consistent with other basilosaurids worldwide. Basilosaurus is my state fossil and the centerpiece of the museum where I do some work. I’ve spent quite a bit of time on them. Including private discussions with Hans Thewissen about that very specimen
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And let’s assume that fossil is 49mya. If anything that would mean there are older Packcetids. Which is a real possibility. There aren’t any Indian Paleocene mammal localities! So we should be very cautious when discussing timeframes with whale evolution. And if I recall correctly when faced with the new date on the Antarctic jaw, the DI said the authors gave it the 40mya date to hold onto its evolutionary interpretation. if that’s the case why would they even announce the discovery? The fact that they did tells me they are doing good, honest science and came to the 40-46mya dates based on the data. Not “evolutionary bias”.
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The actual paper:
http://www.bioone.org/doi/abs/10.5710/AMGH.02.02.2016.2922?journalCode=ameg
In summary, considering that 87Sr/86Sr ratios provided for TELM 4 might be biased (because of potential reworking and oscillation of the marine Sr isotope curve during the Eocene), we interpret the age of the horizon that produced MLP 11-II-21-3 (i.e., TELM 4) as early middle Eocene (~46–40 Ma; middle Lutetian to early Bartonian based on ICS International Chronostratigraphic Chart 2015; Cohen et al., 2013) and follow the most recent chronostratigraphic interpretation for the La Meseta Formation.
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So, I am curious if observers would feel a response to ENV would be helpful. I did not realize it would be picked up by them, but would consider a response if others want one.
Any discussion where genetics is the subject would be helpful to me. I’m just now beginning my genetics studies so a lot of the time I just don’t know how to interpret certain things. So it would be for me. I’d also like to see the waiting time problem
Discussed and thoughts given on that
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Or perhaps, @T.j_Runyon, a definite reality … according to these resources…
[My apologies… I reversed the numbers 48 and 56 at the start and end of the Ypresian Age ]
On the subject of whale evolution, there’s a fantastic article out in The Atlantic about evolution and the size of marine mammals. Well worth the quick read!
I can’t speak to the viability of the genetic/mathematical objections for “unguided evolutionary mechanisms” (and would be interested in further specifics/discussion), but supposing it to be true for the sake of discussion, that would be no objection for the evolutionary creationists who believe evolution may have been guided in some way, including possibly the ideas that “natural genetic engineering” mechanisms may have “guided” cells and their DNA to make quasi-intelligent changes that go beyond pure lottery-like random probabilities.
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I think you have some fair points there @joshuahedlund; last night my attention was drawn to the mathematical arguments that were referenced by EN. EN was super excited to find this paper for example:
I had no idea exactly how to read the paper, so I wanted to see some experts writing on the topic. One that I found was this critique of the PLOS One paper:
http://serialmentor.com/blog/2014/9/24/a-critique-of-chatterjee-et-al-the-time-scale-of-evolutionary-innovation-plos-comp-biol-2014
Also a great point regarding how scientists are honestly piecing together the fossil record. I think that most people have the idea though that paleontologists are just randomly ordering fossils so as to support their ‘religion’ of evolution. I suppose the great irony is that it is not scientists who are doing such, but typically those accusing scientists of doing such.
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Okay @joshuahedlund and @pevaquark this might count as a critical mass of interest. I may write something more detailed about the waiting time problem in the coming weeks.
Please do. That’s a topic I haven’t seen much written about on the evolution side.
I believe the more we remind our YEC cousins of this, the more we’ll progress making getting the next generation of Evangelicals to embrace our God-Guided logic!
I think it is important to describe the borders that science is working in. The scientific description of unguided evolutionary mechanisms is focused on observations, not metaphysics. IOW, scientists are saying that evolution doesn’t LOOK like it is guided, or that there isn’t any positive evidence for guidance. Science doesn’t go as far as saying guided evolution is false in a metaphysical sense. Scientists aren’t trying to falsify every single explanation out there. They are more interested in testing one idea and seeing if observations are consistent with that idea.
The type of positive evidence scientists would accept for guided evolution is the same DNA sequence or the same adaptation appearing in distantly related organisms and the lack of the same adaptation in more closely related species. IOW, they would be looking for clear examples where the predicted nested hierarchy is violated. Perhaps there are other types of scientific evidence that could support guided evolution in a scientific sense, but that is the first example that popped into my head.
As to Shapiro’s “natural genetic engineering”, that is unguided evolution. Shapiro tries to put fancy labels on biological mechanisms to make them look like they are guided when in fact they aren’t. For example, the types of mutations that Shapiro points to are still random with respect to fitness.
Understood… Yet it also seems quite different and much more interesting than what YEC’s are typically thinking of when they say “unguided evolution”!
Almost all of biology is more interesting than what YEC’s typically think. 
On a more serious note, you are absolutely correct. Jumping transposons, phage insertion, homologous recombination . . . these are all very complex mechanisms that are very, very interesting. Some of the ES crowd (the Third Way, or Extended Synthesis) take advantage of the fact that some do have a simple view of biology to act as if biologists have been hiding something when they have been doing nothing of the sort. They talk about all of these complex DNA interactions, but miss the most basic question: Are the mechanisms producing these mutations guided by fitness in any meaningful way? In all of the examples I have seen, there is no evidence that they are guided by fitness. A new transposon insertion is just as likely to be detrimental or neutral as it is beneficial, as one example.
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