"There is no such thing as a 'transitional fossil'..."


(Jay Johnson) #103

Forget Tiktaalik. As a notable transitional fossil, I nominate the H. sapiens from Jebel Irhoud, Morocco.

https://www.nature.com/articles/nature22336

Neanderthal and all previous hominins had an elongated skull and a large face, compared to the smaller face of H. sapiens. The skull from Jebel Irhoud, dated around 300,000 years ago, has a small face, like us, but an elongated skull, like Neanderthal. Additionally, all H. sapiens infants are born with an elongated skull, like Neanderthal and every previous hominin, but the rapid growth of the infant sapiens’ parietal lobe, cerebellum, and frontal pole reshapes the skull into our distinctive globular pattern by the first birthday.
Comparison%20of%20skulls%20captioned

From the abstract of the linked article:

We identified a mosaic of features including facial, mandibular and dental morphology that aligns the Jebel Irhoud material with early or recent anatomically modern humans and more primitive neurocranial and endocranial morphology.


(Daniel Fisher) #104

This is very insightful, I’d never thought of that before. But yes, when given a moment’s thought it is clear… a cladogram by definition assumes common descent. You could clearly take modern cars vs earliest automobiles and everything in between, put our specimens into such a function, and determine which families are related to which, which descended from which.

It probably may have a degree of accuracy in detecting when various design innovations were introduced, and which families are in some sense related. But yes, the entire schema depends upon the assumption of common ancestry.


(Matthew Pevarnik) #105

You wouldn’t need to find much of anything. 30 loads of soft tissue all over the place, lots of carbon in dinosaur fossils, and we definitely would’ve sequenced entire genome’s by now. But those things are relatively rare, and depending on the conditions we could find some amount of soft tissue but none of the other two things.


(Matthew Pevarnik) #106

No it doesn’t. There are entire courses and textbooks and it’s done in every single paper will you test to see if you have a true tree like signal at all.

And you would learn nothing because cars cannot reproduce and can’t have random mutations, gene duplication, exon shuffling, etc.


(Chris) #107

An interesting post that has made me think a bit more about the subject.
When there is a cross between two varieties with different characteristics we can get a blend of characteristics or a mosaic, or both, within the offspring. This applies to dogs, cattle, and people; but we don’t refer to these as being transitional. In the photo below the parents both have white mothers and black fathers. Are they Transitional? Their twin daughters are black and white (and beautiful)

Is this specimen of H. sapiens from Jebel Irhoud, Morocco transitional or does it have a mix of features because of mixed ancestry? From a quick check on line both Neanderthals and H. Sapiens predate this find so I think it is probably a mosaic of features due to cross breeding and so the specimen is not transitional.

Even today we can look around the world and find a huge diversity in the appearance of humans; from a black pygmy to a blonde Scandanavian. When looking at fossils it be be hard to distinguish different species and in species variation, and even variation due to different ages. I read some time ago about how different “species” of fossils were being consolidated into a single species as further finds showed that the differences were just part of normal variation.

So once again I say that intermediate in form (mosaic or blended) does not necessarily mean that it is transitional.


(Chris) #108

DNA degrades quite rapidly so dinosaurs buried over 4000 years ago in Noah’s Flood are unlikely to have intact DNA to sequence. It’s quite surprising that soft tissue has been recovered from a number of fossil dinosaurs.

Yes, you can for instance calculate a consistency index, retention index, or a rescaled consistency index, or log Bayes factors as Ewart did in “The dependency graph of life”. In general these show that phylogenetic trees trees do not score particularly well, although some will score better than others either due to chance or to careful selection of the traits being considered.

cladogram

[klad-uh-gram, kley-duh-]

noun Biology.

a branching diagram depicting the successive points of species divergence from common ancestral lines without regard to the degree of deviation.

Cladogram Definition

A cladogram is a diagram used to represent a hypothetical relationship between groups of animals, called a phylogeny .


(Jay Johnson) #110

I’ve done much more than a quick check online. Neanderthals originate long before the Jebel Irhoud find, dated at 300 kya, but if you can find a fossil classified as H. sapiens prior to Jebel Irhoud, that would be news to me (as well as the rest of the scientific establishment).


(Chris) #111

The age of speciation of H. sapiens out of ancestral H. erectus (or an intermediate species such as Homo antecessor ) is estimated to have been roughly 350,000 years ago. Wikipedia.

Well I know Wikipedia is not a particularly reliable source but it does say H. sapiens are older than 300 kya.


(Matthew Pevarnik) #112

You give me Ewert and ignore everything else that is done in the field once again, dismissing it this time with the suggestion that scientists intentionally choose what traits they want to compare to get ‘stronger tree signals’ or just getting lucky.

Indeed. So how then should one explain this? As a nice recent paper summarized when they examined exactly what we are seeing in fossils and the result was consistent with previous hypothesis of preservation:

Soft tissues were present in all modern samples, but [found] only in those fossils from oxidative settings.

A pop-science version of the paper: https://www.earthmagazine.org/article/dinosaur-soft-tissues-preserved-polymers

How rapidly does it degrade? Here’s a nice example recovering DNA from a 300 kya cave bear in Spain outside of permafrost preservation: https://www.pnas.org/content/early/2013/09/04/1314445110.abstract

A recent paper looking at the read-fraction and amount of DNA in a marine setting beginning a few thousands years ago to a million years ago:

Notice the large amount of DNA that should be present in all fossils that were buried by a flood, i.e. in a marine environment. Sorry @aarceng, dinosaurs didn’t live just 4,000 years ago.


(Phil) #113

Sometimes it is, sometimes it is not. Chris, pigment variation is not remotely related to being a different species. While there is diversity within a species, transitional species vary in more fundamental ways.

Actually, DNA is frequently found in teeth and bones far older than 4000 years. Of course, 4000 year old bones are pretty much still bones, not fossils. The Neanderthal genome was sequenced from a 50,000 year old finger bone, just to give one of many possible examples. Of course, I am sure you also reject well documented dating techniques too, so am probably just wasting time and bandwidth.


#114

That’s the point isn’t it… It’s amazing what an impact the original assumptions have on the validity of the conclusion.


(Matthew Pevarnik) #115

Indeed. It turns out to understand how genomes change you actually need to include the mechanisms for how genomes change instead of pretending living things are automobiles that were intelligently designed.


#116

the problem with your diagram is that it has too few samples from recent times to indicate a reliable retention curve. You only have one data point less than 1000 years, and no others less than 2000 years old. The assumption of age is made and samples thus dated, but a reliable retention curve needs to come from animals that are known to be less than 1000 years old, or at least less than 2000 years old. If such a curve is syncronous with the table you printed, then you might have a point.


(Matthew Pevarnik) #117

Are you trying to figure out how the samples were dated? There are two main ways that this was done. One was through paleomagnetism (i.e. the Earth’s magnetic field has changed polarity in the past and rocks record this). You find something like this:

You can also use a technique called biostratiagraphy where you carefully examine which species appear in which strata which helps you date the strata (you can also use radiometric dating of course as there were decent amounts of Potassium, Uranium, etc.). Comparing the two methods you get something like this as a function of depth:

Feel free to poke around the summary of the expedition if you like more detail: http://publications.iodp.org/proceedings/323/EXP_REPT/CHAPTERS/323_101.PDF


#118

No. I am saying that to validate the curve, many more recent samples need to be evaluated, placing them on the curve with dna residue percentages. In other words, what does the curve show for samples that are 1000 years old, or less, and how does it correspond to the curve/line on your graph.


(Jay Johnson) #119

The “age of speciation” is a calculation, not a fossil. The oldest sapiens fossil is the 300,000-yr-old Jebel Irhoud discovery. Of course, an even older specimen might be found, but it hasn’t happened yet, to my knowledge.


(Matthew Pevarnik) #120

The curve is perfectly fine as is. The dates are cross checked using multiple independent means. That is significant amounts of DNA found in such marine sediment going back long periods of time. Another paper looked at a more recent time frame though used a different unit:

Again going back tens of thousands of years still even had ‘operational taxonomic units’- being able to not just find DNA but extract information from it about the organism.


#121

Unfortunately, it is not perfectly fine. The only way to verify decay rates is within a 1000 year timeframe. Your other example does not do this, since it does not compare samples from similar species at various times, with regard to percentage of dna decay or dna survival. First of all, a fifty year time period should be established, measuring decay rates at least every five years, preferably every two years, with the proper statistical numbers of samples under controlled conditions. Then, since it would be unreasonable to attempt a longer controlled experiment, various similar species samples from known ages, say every decade if possible, to 200 years of age. Perhaps beef specimens, or bison, would be a good example, since it is more likely possible to actually verify age of samples. Perhaps humans, since date of death is often documented on tombstones. In north america, at least 500 years back would be possible, and in Europe, much further than that. If this curve matches the ones for the supposed age of 65,000 year or 65 million yr old samples, then you have a valid point. Otherwise, the assumption will be that dna cannot survive that long, and therefore the proposed age of fossils/samples is erroneous. To say that the radioactive decay rates are more certain than the biological organic decay rates, is invalid.


(Matthew Pevarnik) #122

Not even close. We can try to break radiometric decay in very extreme conditions and we’ve failed. But yet the breakdown of DNA is rather sensitive to conditions.

In your eyes, sure. If you happen to find some rock that has DNA in it that’s a thousand years old, and then some more rock that’s 5,000 years old with some DNA and then some rock that’s 100,000 years old in the same stratiagraphic sequence, you can compare the types of fossils found and the concentrations of DNA over time. The initial location was particularly nice being a marine environment with fairly constant sediment deposition rates ~26 cm/yr.


#123

Have you included the probabilities for these mechanisms somehow randomly forming, in your calculations. For example, these mutations are not just from a random number of bases combinations passing by and accidentally falling into place. The transcription errors, and then the corrections, also fall into the overall probabilities. These things reduce the likelihood of beneficial mutations even further. In addition, what we call a beneficial mutation is subjective many times. What is beneficial to a worm, would not be beneficial to a cheetah. And vice versa. Or in another case, something that is less beneficial, may still survive, because the environment is large enough for several options. As in the same environment may be able to support both white-tail and mule deer and elk and woodland caribou. There is no real distinction about what is more or less beneficial in this case.

Ironically, if we assumed human evolution from some hairy ancestor, we would see that in order for the benefits of a bigger brain to be advantageous, it would have to be accompanied by a weaker body, and by hairlessness, a vulnerability to weather. Otherwise, there would be no need to use the bigger brain to survive, and thus no advantage to the bigger brain. The hairy human with powerful hands and feet and long tail could simply survive in the open like all the hairy apes, instead of wearing clothes, building houses, growing gardens, and herding sheep.