This article points out that evolution is not random. Of course it isn’t! There is selective pressure to develop traits to survive in the environment. It even goes into gene duplication and how that allows the organism to “experiment” with the protein while keeping a full functional copy intact to survive.

Think about that. Why does the extra copy need to be “experimented” on if the mutations were purposeful? If it were non random, you would expect that the mechanism of evolution would know what it needed to mutate and then just do it. But it doesn’t. So the gene duplicate is used to create random mutations – experiments – until a protein that works really well under the selective pressure is arrived at by chance. That organism will then have an advantage over its competitors and the gene duplicate that was randomly mutated will proliferate throughout the population.

This article is about convergent evolution and how environmental stress directs common solutions to common problems. And it is absolutely no different than how bacteria develop antibiotic resistance. There is also epigenetic and proteomic level control which evolved from random mutations to create system which limits the randomness and arrive at solutions more quickly but still as a result of random mutations.

You’d do better understanding more fully why this is than continually trying to dig up articles that you think might disprove the random part of things. It is the fundamental driving force of evolution, guideed by natural selection, and modified by epigenetic and proteomic factors. That is simply a fact, Sonic. No ifs, ands, or buts about it.

Random simply means that the outcome was not determined by its consequences.
You want a coin to flip heads because you win if it flips heads, but the outcome is 50% heads, 50% tails regardless.

The article touches on epigenetics but epigenetics is fully and completely explained by random mutation and non-random selection. The epigenetic mechanisms were put in place in the genome by random mutation and non-random selection through evolutionary history, and the epigenetic mechanisms themselves clearly consist of random mutation and non-random selection, though this time within the organism itself. It’s always still a coin flip or a throw of the dice, with the environment selecting the winner.

But the article is mainly about convergent evolution. As if that contradicts the prevailing paradigm. All organisms are made from DNA, so its no mystery that different organisms converge on the same “good tricks”.

Here is an experiment that goes directly to this point–
http://www.sciencedaily.com/releases/2012/10/121025130922.htm
Title–
“Far from Random, Evolution Follows a Predictable Genetic Pattern”

Yet…

a new species did occur in a single generation. But that is not a dog giving birth to a cat. Not even remotely close. I never said that speciation in a single generation would falsify evolution. I said that a dog giving birth to a cat would.

And yes, no fossils ever. As I said, if you read the rest of the post, the author clearly demonstrates that, still, no fossils ever have been found out of place. The apparent paradox of ghost lineages always ends up becoming resolved (eventually). That is why the paragraph you picked was cherry picking – it was not representative of the thrust of the article nor the author’s intent. That is why I directed you back to Novella’s post on paradox – the “ghost lineage” is just a term given to a placeholder for the yet-unknown lineages.

I did misunderstand your point. However, your examples were also incorrect.

If you say that something never happens and I show an example of where it did– even one time– how is that cherry picking?

I point out that one species gave birth to a different species in one generation (a dog gave birth to a cat)..
You are the one who claimed this would falsify evolution when in fact it clearly does not.

You claimed that ‘no fossil has ever’… but clearly this is not the case (the need for ghost lineage). You said this would falsify evolution- just one instance. I did not and it does not.

You are claiming my examples falsify evolution.
I say my examples don’t. And clearly they don’t.

It is your claim that these examples would falsify evolution that I am suggesting is incorrect.

The real problems begin where we have a good fossil record and a well established phylogeny but the two are still at odds. We can’t immediately think that our phylogeny is amiss nor that our well scoured rocks are failed to preserve the well represented (or we have not found it). The truth however is that these situations are incredibly rare and to be honest I cannot think of an obvious candidate to use as an example here</B though they abound for others with either phylogentic issues or preservational ones. Haldane’s rabbit is the only think I can think of and that itself is a hypothetical example.

So the reference you are throwing at me to disprove my statement regarding the fossil record in fact… supports my statement about the fossil record. It discusses nuances and finer points, but is clearly demonstrating the integrity of the process and teh veracity of evolution.

Yet you cherry pick the one paragraph in the entire piece that seems to support your statement. Why is that sonic?

But just how much of a problem is this? Are these really very important and what do they mean? Well that all (inevitably) depends on the exact situation which is a combination of phylogeny and preservation. Generally however I would say that they are interesting but not necessarily that important –they tell us that there is potentially a problem with either our understanding of the fossil record or our phylogenetic hypotheses and neither of these is especially enlightening – we know this already – and some circumstances are pretty much unavoidable.

In short, refer to Dr. Novella’s post about the paradox paradox. This author is not discussing finding a fossil that is actually out of order. It is about discussing potential discrepancies in the predicted phylogeny and an incomplete fossil record (i.e. ghost lineage). It is a hypothesis generator that tells us there is some extra information to look for, not something that demonstrates to us that evolution is wrong. Note he even specifically references Archeopteryx. Also note that since that time, new fossils have been discovered that fix that issue quite nicely – in other words, filled in that area where we lacked knowledge.

These discrepancies are also for cladistically close species. You’ll never find such an issue over bigger time scales.

“The crux of the ghost lineage problem is where we have disparity between where we find certain organisms in the fossil record, and where we think we should find them. Everyone agrees that plants are older organisms than animals and thus we should find plants earlier in the fossil record than animals and we do, but we also think that birds evolved from derived maniraptoran theropod dinosaurs, yet we find birds (well, OK, Archaeopteryx) *before* those dromaeosaurs and troodontids that they supposedly evolved from.”

No – a primrose with double chromosomes is still a primrose. That is not speciation, and it is not evern remotely an example analagous to a dog giving birth to a cat.

Which was in response to:

One observed instance of speciation is the evening primrose. In this case we find a variant that has 28 chromosomes instead of 14 as a result of a gene double.
In other words a dog gave birth to a cat.

I did not look up the case of the primrose specifically. However, chromosomal doubling or other aneuploidy in plants is common and does not de facto lead to speciation. It is a common step in speciation, and in fact is often the source of novel proteins. But it does not inherently mean speciation (the same way that a Down syndrome child is still a human). I have been proven wrong that in this case of the primrose it did.

The reason that it did in this case was because the aneuploid varietal could not breed with the parent population but could breed on its own (i.e. not sterile) – that is the definition of speciation. I’ll be honest that I did not look at the case of the primrose itself, because I focused on the part of sonic’s post which I bolded above.

A primrose speciation event by chromosomal doubling is in no way even remotely analagous to a dog giving birth to a cat. How you managed to assert that is completely beyond me. If the doubling led to the primrose becoming an apple tree then that would be analagous.

Hopefully that clears up that. Interesting though, that after all this time the response given was to pick a nit (a valid one, albeit) rather than addressing a much more salient point:

But fossils are found out of place regularly. One method of dealing with this is called ‘ghost lineage’. So not only are fossils found out of place– there is a standard handling for it.

to which I responded

And indeed, there has never been one single fossil discovered out of geological space ever. Not one.