Evolution under the microscope

Homology refutes evolution

2011-02-07T12:19:00.000-08:00

Homology is commonly cited as demonstrating, or even proving, common descent and evolution. But there is substantial evidence showing that supposedly homologous structures in fact are not; and in doing so this provides compelling evidence against both common descent and macroevolution. Let me explain:

Homology - what is it?

Historically, homology is simply similarities of biological structure. Probably the most widely-used example to illustrate this is the skeleton of vertebrates, especially the forelimb of tetrapods (vertebrates with four limbs): despite the substantial differences in overall appearance of e.g. a horse’s foreleg, human arm, bird’s wing and whale’s flipper - the underlying bone arrangement is remarkably similar.

The theory of evolution seems to provide an elegant explanation for these similarities. It proposes that the tetrapod leg, from its first appearance with the early amphibians, as their descendants diversified, was itself progressively modified to adapt to differing uses. Similarly, the supposed evolution of tetrapods from fish is supported by the similarities of skeleton of all vertebrates. This evolutionary explanation has become so widely accepted that it now defines homology as referring to those organs which have been derived from the same structure in a common ancestor.

That is, over the course of evolution, modifications of the embryological developmental processes have resulted in divergence from the common embryological source to give the range of modern day organs. And with this evolutionary account of homology, embryology acquired an important role in identifying and interpreting homologies. The point being that, even if adult structures look rather different (wing, flipper, arm), if they are homologous then they will be derived from equivalent embryological sources.

Conversely, even if structures from different species look similar, if they have developed from different embryological tissues then they would not be regarded as homologous, but due to convergent evolution. A good example of this is the vertebrate eye and that of the cuttlefish (a mollusc related to squid). In overall structure they closely resemble each other, notably in having a lens and iris, are equally specialised and with comparable performance. But they are not considered to be homologous, as there is no doubt they have arisen quite independently in separate phyla (chordates and molluscs) which have completely different body plans. And there was no common primitive eye from which they have both evolved.

Homology - the inconvenient truth

Although most evolutionary texts convey a consistent and hence persuasive picture of homology, there are in fact many substantial anomalies. In particular, as we discover more of how tissues are formed embryologically, increasing doubt is being cast on much of the homology that has been perceived for so long at the morphological level.
Notably, in view of the importance attached to the apparent homology of the vertebrate skeleton, and the weight given to embryology for identifying homology, it is especially relevant that vertebrae – a major component of the vertebrate skeleton – form embryologically in significantly different ways for different classes of vertebrate (such as mammals, birds, amphibians and fish), and even from different groups of early embryonic cells. (For example, see Vertebrates: Comparative anatomy, function, evolution by K. Kardong.) This clearly shows that the vertebrae of these different vertebrate classes are not, in fact, homologous - and hence that these different groups of vertebrate do not in fact share a common vertebrate ancestor, despite their superficial similar appearance and contrary to the commonly held view.

Taking this further, in the course of embryological development the members of different classes of vertebrate pass through a similar-looking stage (called the phylotypic stage), which is seen as clear evidence of their common ancestry. However, what is confounding (from an evolutionary perspective) is that even though the phylotypic stage looks similar, and we would have expected it to be formed from a fertilised egg in substantially the same way, there is, in fact, remarkable diversity, including some fundamental anomalies. The fact that the phylotypic stages are formed in different ways prima facie at least undermines, if not completely negates, the notion that they are derived from a common ancestor. And there are similar anomalies in other phyla, not only the vertebrates.
This is not just putting an anti-evolutionary spin on the facts. Here’s what evolutionary biologist Rudolf Raff had to say:
The process of early development from the egg to the phylotypic stage should be at least as conserved as the pattern of the phylotypic stage. One might reasonably expect mechanisms of early development to be especially resistant to modification because all subsequent development derives from early processes.

Homology - why the evidence is important - and hence ignored!

The evidence from homology - or, rather, the lack of it - is very important. Although some people try to dismiss the ‘intelligent design’ case against evolution as a ‘gap’ argument, this excuse is not available over homology. The fact that apparently homologous organs such as the vertebrae in fact have proved not to be, not only removes circumstantial evidence in support of evolution - it constitutes clear counter-evidence against the organisms concerned having evolved from e.g. a common vertebrate ancestor. This evidence unequivocally refutes the theory of evolution.

And this no doubt is why so few, including professional biologists, know about these anomalies - they are kept safely out of the limelight so as not to upset the applecart. As mentioned above, textbooks on evolution only cite the evidence that supports evolution. How many who are reading this article knew previously about the anomalies of so-called homology?

Peer Review

2010-04-03T11:43:00.000-07:00

In the preceding post (below) I mentioned what I think is a key failing of evolutionary scenarios, such as that of the eye by Nilsson & Pelger - they completely ignore what we now know of the genetic and molecular mechanisms that are essential for forming biological tissues. And along with this they ignore the fact that the evolution of substantially new biological structures, such as eyes and feathers, would require new genes to arise.

And my point here is this: this knowledge has been well known for at least a generation; yet, not only did N&P (and authors of comparable scenarios for other organs) feel free to ignore this, but presumably the reviewers of their paper were happy to overlook this oversight too. And, we should note, it wasn’t published in some minor or obscure journal, but in the prestigious Proceedings of the Royal Society of London.

Before I comment further on peer review, let me also mention another serious flaw in the authors’ rationale. Their aim was not only to show what they considered to be a plausible scenario for the evolution of an eye, but also to estimate how long it would take - to show that there was plenty of geological time for it to happen. But their method was seriously flawed: their calculations used an equation (in Falconer’s Introduction to Quantitative Genetics) formulated to estimate the time to effect change through domestic breeding.

First of all, this reinforces the point I made previously - that their model for the evolution of an eye is based on selection from an already existing gene pool - completely ignoring the fact that a new organ such as an eye will require very many new genes (which are prohibitively improbable to arise - a central theme of my book).

Second, their model assumes that only those organisms having a variation that confers at least a 1% improvement in vision will contribute to the next generation. This is the sort of thing a breeder can put into practice, but totally unrealistic to think that natural selection (which of course is what the evolution of the eye would have had to rely on) will operate this way - most of the mature individuals (even those with reduced visual acuity) in a population will have some offspring.

So these criticisms completely undermine their claim that their calculations are a ‘pessimistic’ estimate of the time for an eye to evolve. Quite the opposite!

This also gives some insight into peer review: Presumably the reviewers were so happy with the overall message of the paper that either (a) they didn’t examine it too closely, and/or (b) they were aware of its serious shortcomings but chose not to stand in the way of a paper which said what they want to hear. At very least It shows that ‘peer review’ is not the independent objective assessment it’s claimed to be.

And its not just the reviewers who are at fault. This paper is referred to widely to support the notion that eyes could have evolved readily. Have none of these bothered to take a careful look at what N&P actually proposed?

Eye Evolution

2010-04-03T11:29:00.000-07:00

A good example of where belief in evolution is maintained because people aren’t prepared to look at the detail is in the supposed evolution of new organs such as the eye.

The eye is the classic example of a highly specialised organ, considered by many pre-Darwinian scientists such as John Ray as incontrovertible evidence of design in biology. Even Darwin recognised that the eye was a challenge to his theory, but in the Origin speculated how it might have arisen progressively from a simple light-sensitive tissue through a series of variations.

In the 1990s a couple of Swedish scientists, Dan-E Nilsson and Susanne Pelger (Proceedings of the Royal Society of London Series B - Biological Sciences, 256:53-9), expanded on this sort of scenario, illustrated as follows:

Starting from a patch of light-sensitive cells (which is a huge presumption in itself, though I can’t expand on that here) it is envisaged that an eye evolves by a flat patch of cells becoming a depression, which gradually deepens into a small pit (a to c), the neck of which then narrows (d). Each of these stages, taking place over several generations, is driven by the advantage of increased optical acuity (better resolution). When this stage has been reached, further improvement can be achieved only by addition of a lens (e), and the authors boldly assert that ‘Even the weakest lens is better than no lens at all, so we can be confident that selection for increased resolution will favour such a development all the way from no lens at all to a lens powerful enough to focus a sharp image on the retina.’

The totally unjustified assumption in this scenario is that if a variation will offer some advantage, then we can be sure that it will arise. No thought whatsoever is given to the crucial question of how those variations will arise. I think this blind spot (!) has arisen for two reasons.

First, before we knew about genetic and molecular mechanisms, it was thought that biological tissues were innately plastic in the sense that variations would arise spontaneously, and favourable ones could then be passed on. However, we now know that the formation of morphological structures – whether it be an eye, feather or leaf – is not by some sort of vague plasticity, but through the closely orchestrated action of many genes. So new structures need new genes. But in the above scenario, all that we have learned in the last 50 years about the biochemistry of tissues and the molecular mechanisms involved in forming tissues is totally ignored.

The second reason arises from the fact that much variation is possible through the mixing of genes that are already available. For example, it’s been known since well before Darwin that domestic varieties of crops and animals can be developed by breeding selectively from those individuals which have the desired variations (which have arisen naturally). But it was also well-known that there are limits to the amount of change that can be achieved this way. Which is why, although artificial selection could validly help to illustrate natural selection, Darwin’s contemporaries also knew that domestic breeding could not support changes such as the evolution of new organs. We now know why: new organs need new genes and molecular mechanisms to construct them - which are not available in the genomes of the original parents.

This oversight is illustrated by the fact that the above-mentioned authors’ calculation of the rate of eye evolution is based on selection from an existing pool of genes. Whereas there can be no doubt at all that the evolution of an eye would require very many new genes – for several proteins used exclusively in the eye, and for the molecular mechanisms that construct the eye in the course of embryological development. So their comment about a lens arising simply because it would be advantageous to do so is just ignorant wishful thinking - scarcely science at all.

There are so many speculative scenarios for the evolution of new structures - whether they be for eye, wing, feather, limb or whatever - but they are no better than those available in the 19th century - because they are based on the assumption that biological tissues are plastic, and completely ignore the genetic and molecular implications. If proponents of evolution want their scenarios to be taken seriously then they really do need to take on board the genetic and molecular detail.

Design or Apparent Design?

2008-02-08T03:53:00.000-08:00

It’s my intention to debate the issues, not personalities; but as Richard Dawkins is such a popular advocate of evolution, I’m going to start by referring to some of the things he says; partly, because I agree with some of them.

In particular, I agree with him that the biological world looks designed, but that the subjective perception of design in itself is not conclusive. In The Blind Watchmaker (Ch.2) he calls this the Argument from Personal Incredulity - e.g. ‘I don’t see how something as beautiful / complicated or whatever as ... could have evolved’. As he says, there’s not much point in saying that something-or-other could not have arisen by chance, because no-one is seriously suggesting that a mammal, flower, or even bacterium has arisen spontaneously by chance.

We need to fully take on board the non-chance process of natural selection and its potential for producing a very unlikely end-product through a long series of small stages where each offers a small advantage over its predecessor. As he puts it in God Delusion (p 121, my emphasis) :

What is it that makes natural selection succeed as a solution to the problem of improbability, where chance and design both fail at the starting gate? The answer is that natural selection is a cumulative process, which breaks the improbability up into small pieces. Each of the small pieces is slightly improbable, but not prohibitively so.

But it seems to me that he is so taken with the elegance of the idea of evolution that he assumes it must be true and does not actually expose it to scrutiny. That last sentence which I emphasised is merely asserted, never substantiated or even scrutinised. He says we should examine the issue objectively, but doesn’t practise what he preaches!

I have also read Dawkins’ The Blind Watchmaker and Climbing Mount Improbable, both of which extol the power of cumulative natural selection, yet neither examines the crucial issue of the likelihood of occurrence of the variations on which natural selection can act. Despite his comments about breaking down immense improbabilities into smaller steps, nowhere is there any attempt to quantify the probability of those steps. In discussing the possible evolution of the eye (Watchmaker, Ch 4) he assumes that it can be broken down into infinitesimally small steps (in order to improve their probability); but this is not correct because of the discrete nature of genes.

Bertrand Russell said:

This [design] argument has no formal logical defect; its premises are empirical and its conclusion professes to be reached in accordance with the usual canons of empirical inference. The question whether it is to be accepted or not turns, therefore, not on general metaphysical questions, but on comparatively detailed considerations.

I agree, and I sought to examine the theory of evolution in the necessary detail in my Evolution under the microscope. But Dawkins never examines it in detail; he merely relies on on the elegance of the theory, and polemic (and, sadly, ridicule).

Design or Apparent Design? - the answer is in the detail.