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(092112)

Molecular Evidence


Questions:

Short Answer:

The chemical composition of molecules from living cells— when used to compare species to species, be these species closely related or taxonomically distinct— make for yet another unique perspective on origins. Any changes in genetic codes or protein composition over time tell us something about life's origins. As in many areas of discussion on origins, we find that much of the scientific data is initially considered in light of what evolution theory would require. The real question to ask, however, is there an alternate interpretation from these data? Given evidence for considering alternatives, do we then find ourselves facing the task of reviewing life's entire knowledgebase in terms of some other explanation for origins?

A short answer can be framed like this: If we expect that evolution theory fits with all the data to be collected, scientists will seek to fit the data to the theory. Yet, as recent data are amassed, the fit is not precise to this expectation and in some places is contradictory. So, NO the evidence does not necessarily have to find a fit. Again, the molecular data are commonly interpreted in light of expectation (i.e., assumption). That aside, the evidence considered here forces us to rethink origins based on what is now discovered at the molecular level.

As biophysicist Dean Kenyon, a once-prominent origin-of-life researcher, said concerning his own discipline several years ago: "The more ... we have learned in recent two or three decades about the chemical details of life, from molecular biology and origin-of-life studies... the less likely does a strictly naturalistic explanation of origins become." Meyer (CH) Page 68

There continue to be observations that do not fit what Darwin suggested would come by science and in time. What would he have told us if he had some insight on future results from molecular biology. He did speculate the fossil record would reveal a continuum of forms leading from species to species, phyla to phyla, from ancestral form to the diversity of life we see. This paints the picture of evolution's 'tree of life' (<< considered in another article). Taking Darwin's inclination we might then expect he'd say there would be a molecular pattern that also shows the imprint of this evolutionary trend over time. But what if it is a different sort of pattern? Without the expected trend at this level of detail— along with the absence of fossil evidence Darwin presumed would be forthcoming— we are left with one more aspect of an evolution scenario that is mysterious or unsupported.

There is more in the way of recent work to describe here (relevant content will be added in the future), but the examples noted here are truly remarkable. The observations reveal a separation of species as something equidistant (this pattern appears in protein amino acid sequences of higher life forms) or as a web of molecular evidence that shows a cross linking between species (this especially with regard to single cell life forms; e.g.:> see Chapter 3 of Icons of Evolution and the description of the highly cross branching 'molecular thicket of life'). Both of these patterns in Darwinian terms are 'the unexpected.'

Consider This:

The molecular evidence that scientists now gather comes from modern technologies for biochemistry, genetics, genetic engineering, and other areas of research. Mostly, this concerns the DNA and RNA involved in the genetic code, in the processes that build cells and organisms, and further that direct life's activities. Other molecules are important to these studies and much is to be learned in relation to origins or evolution by evaluating the composition and structure of proteins. The genetic code and the information within are topics covered in another feature article (DNA and Information). When considering the standard story for evolution and 'life's tree,' one finds evidence for the lineage of life forms that does not entirely support use of the tree illustration. In this case we encounter terms like hierarchy or typology which suggests life forms are separated into unique groups without the evidence that ties life back to a common ancestral form:

We have seen that at a morphological level the pattern of nature seems to correspond reasonably well with the old nineteenth-century typological model. Nearly all known groups appear to be isolated and well defined and clear sequential patterns whereby one class is linked to another through linear series of transitional forms are virtually unknown. Moreover, classification procedures invariably result in orderly hierarchic schemes from which overlapping classes indicative of sequential relationships are emphatically absent.

We cannot, for example, quantify the difference between a cat and a dog and compare it with, say, the difference between a cat and a mouse. We assume that a cat and a dog are closer than a cat and a mouse, but how secure are such judgments? Denton (ETC) Page 274

The statement above reflects what we know from the physical form of beings. But within these forms are chemical entities that can further serve as added evidence to unraveling information on origins. The scientific revolution, with all the new technologies— those that sequence DNA codes, model proteins in three dimensions, etc.— present us with a new way to look at organisms. During the mid-20th century, for example, the amino acid composition of hemoglobin (specifically the order of amino acids making this unique protein) revealed that this molecule was not identical from species to species. Might the differences reflect change over time much like evolution theory would suggest for life in general?

Scientists have taken the amino acid sequences and lined them up to compare not only the differences but also to see how such differences might correspond to the biological origins of the organisms from which the particular hemoglobin molecules were taken. The comparisons here lend themselves to something we can quantify— by counting the differences. That is, 3 amino acids may be different for two of the hemoglobins from two different species, but comparing still another hemoglobin, from yet one more species, one might identify a larger number of amino acids that differ. The differences make for a score card of sorts. The amount of difference makes for a means to compare the organisms that contain each type of hemoglobin. But do these differences trace a pathway for evolution? Well, first off, let's consider what's changing here?

figure 235

AA1
AA3
AA6
AA10
AA2
AA3
AA16
AA1
AA2
AA14
AA3
AA20
AA1
AA5
etc.

Note that a protein molecule overall has certain amino acids ( AAs) in a sequence that also contains an 'active site' that must be conserved — that is, must not change — to sustain the protein's function.

Amino acids outside such a region may be swapped with a number of other amino acids without affecting the protein's role in cell metabolism.


From the 1960s and on, amino acid sequence information gathered for a number of proteins provided a growing knowledgebase of from which evolution might well have been confirmed at the molecular level.

If a pattern emerged to compliment the evolution scenario, then the standard story might be etched in stone for all time. Research on missing links in the fossil record— i.e., the transition forms found lacking— might well be a forgotten issue if the evidence made for a certain molecular scenario. But what's been found to date is much like what Denton reports:

... as more protein sequences began to accumulate during the 1960s, it became increasingly apparent that the molecules were not going to provide any evidence of sequential arrangements in nature, but were going to reaffirm the traditional view that the system of nature conforms fundamentally to a highly ordered hierarchic scheme from which all direct evidence for evolution is empirically absent. Moreover, the divisions turned out to be more mathematically perfect than even most die-hard typologists would have predicted. Denton (ETC) Page 277

Evidence from hemoglobin is only a starting point. Other protein sequences were investigated. Cytochrome C was of particular importance because this molecule is widely found in life forms from bacteria to mammals. The cytochrome C molecules in all these life forms are similar in the number of amino acids and likewise all have the active site responsible for biological oxidation that is important to producing energy for the cell. Dr. Denton describes how one can evaluate the differences found for Cytochrome C molecules:

When comparing the a considerable number of sequences, it is convenient to present the data in the form of a percent sequence difference matrix. In the Dayhoff Atlas of Protein Structure And Function (1972 edition) there is a matrix with nearly 1089 entries showing the percent sequence difference between thirty-three different cytochromes taken from very diverse species.

Examination of the percent sequence difference matrix reveals that it is possible to use the cytochrome sequences to classify species into groups and that these groups correspond precisely to the groups arrived at on traditional morphological grounds. It is also apparent that the sequential divergence becomes greater as the taxonomic distance between organisms increases, a finding that would again have been predicted from traditional taxonomic considerations.

However, the most striking feature of the matrix is that each identifiable subclass of sequences is isolated and distinct. Denton (ETC) Page 278

Amino Acid Sequence 1

AA1
AA4
AA11
AA7
AA3

Amino Acid Sequence 2

AA1
AA5
AA11
AA7
AA3

Amino Acid Sequence 3

AA3
AA4
AA9
AA7
AA3

Lets say we are looking at three protein molecules... each from a different group of organism, yet the same biological protein. In this example, there are only 5 of the one or two hundred amino acid (AA) molecules that are linked together to make the larger functional protein. The idea of a sequence difference can be noted when comparing sequence 1 to 2, 2 to 3, or 1 to 3. The colored AAs help us to see where amino acids are substituted for one another. When Dr. Denton writes about the percentage of sequence difference, as given in the examples in this article, he is not saying that exactly the same amino acids are always different, but the number of AAs that change (thus the total percent change) is what is remarkably similar. If one assumes that the molecular change is time related, then more advanced organisms might have a far different amount of change compared to older (ancestral) organisms. But the pattern is one of 'equal distance' as noted in similar percentages of change. This is not what one would assume for evolution.


In other words, the Darwinian approach was to look at the morphology (form) of organisms and to note more complex forms appear as time proceeds to the present. The molecular evidence revels differences that on the surface would seem to agree with evolution theory, but on closer examination indicate a separation of groups and not the emergence from a common ancestral form. The unique aspect of the data here reveal that:

No sequence or group of sequences can be designated as intermediates with respect to other groups. All the sequences of each such class are equally isolated from the members of another group. Transitional or immediate classes are completely absent from the matrix. Denton (ETC) Page 280

Like a fossil record that does not contain the myriad of small changes leading from one group to the next, the molecular evidence reveals differences but yet a pattern without intermediates between groups. We'll refer you to Denton's Chapter 12 for an exact reading of the following example. But here is a clipping of text that indicates the consistency of difference across widely different groups [in ETC see Denton's Figure 12.2 for a comparison between bacterial cytochrome C and cytochromes of a wide variety of eucaryotic organisms.]:

In the list in a Figure 12.2, if three yeasts are excluded from the list, then the remaining eucaryotic cytochromes, from organisms as diverse as man, lamprey, fruit fly, wheat and yeast, all exhibit a sequence divergence of between sixty-four percent and sixty-seven percent from this particular bacterial cytochrome. Denton (ETC) Page 280

Again, we are just taking a glimpse of a more precise presentation by Denton. But he maintains a consistency here in that modern molecular data appear to parallel observations made long before molecular technologies were known to science.

Note how closely the cytochrome pattern seems to correspond to the circumferential model of nature of the nineteenth century typologists. Denton (ETC) Page 280

Typology looks at arranging organisms by types based on their characteristics (traits, morphologies, etc). Adding the molecular picture reinforces what one sees at the morphological level. If this relationship holds across time, then separate groups remain separate from the start and not branching out over time (note diagram below at right with vertical lines depicting origins a the base and each line ascending upward over time without branches. Darwinian theory is represented on the left. The typological observation of separation is further illustrated by the groupings within the boxes at the top right. Each diagram at the right and left only represent a portion of biodiversity not all organisms on earth.).

compare

This adds different perspectives together and reinforces a viewpoint not anticipated by the standard evolutionary scenario. Let's put a text description together with a graphic that has appeared in a number of sources we've encountered.

When the various terrestrial vertebrate groups, amphibia, reptile, or mammal, are compared with a fishes all are equally isolated. The figure below gives the percent sequence difference between cytochrome C in carp and various terrestrial vertebrates. Denton (ETC) Page 285

So, with the carp (fish) in the midst of this example we look in a number of directions to other groups and see protein sequence (percent) differences that are relatively uniform.

------13------> horse (mammal)
carp ------13------> rabbit (mammal)
carp ------14------> chicken (bird)
>carp ------13------> turtle (reptile)
carp ------13------> bullfrog (amphibian)


Okay, this compares fish to other groups. Denton provides a number of other similar comparisons. So, if one looks at the lamprey (cyclostome), a gastropod (mollusk), silkworm, or bacteria... the story is the same... equidistance between compared groups based on the amount of sequence difference in the molecular data!

The point to glean here is that the the sequence differences don't reveal some evolutionary progression over time. That's something we might expect in support of the standard story.

At a molecular level there is no trace of the evolutionary transition from fish --> amphibian --> reptile --> mammal. So amphibia, always traditionally considered intermediate between fish and the other terrestrial vertebrates, are in molecular terms as far from fish as any group of reptiles or mammals! To those well acquainted with the traditional picture of vertebrate evolution the result is truly astonishing. Denton (ETC) Page 285

Denton adds nucleic acids to the picture and again refers to the Atlas of Protein Structure and Function, mentioned above, to make the following observation of a larger molecular database:

Thousands of different sequences, protein and nucleic acid, have now been compared in hundreds of different species but never has any sequence been found to be in any sense the lineal descendant or ancestor of any other sequence. Denton (ETC) Page 289

Similarly, proteins of conifers are as equally divergent as those of the flowering plants, a group which appears to be far more divergent than the conifers at a morphological level. Denton (ETC) Page 290

To be fair, one may say the jury is still out on the approach of classifying organisms by typology. Denton is careful to note this point. Yet, regardless of where typology stands, the molecular data still pose a problem for the Darwinian perspective.

This does not mean, of course, that typology is necessarily correct. But if we accept that closeness to empirical reality is the only criterion by which to judge alternative theories, we would, if strictly impartial, be forced to choose Aristotle and the eidos, in favor of Darwin and the theory of natural selection. There is little doubt that if the molecular evidence had been available one century ago it would have been seized upon with devastating effect by the opponents of evolution theory like Agassiz and Owen, and the idea of organic evolution might never have been accepted. Denton (ETC) Page 290

Denton further discusses how a divergence of sequences might appear in proteins in various species over time. He introduces the concept popularly known as the 'molecular clock hypothesis' (Denton (ETC) Page 295). The idea here is that molecular changes occurring in a way that tracks with time. Yet, the observed molecular diversity seems to suggest a kind of constraint is applied. The alterations in molecular sequence are not simply playing out over linear time... as might be expected for a clock scenario. And each protein seems to have its own clock running independently of other clocks! No one knows how this works!

Rather than being a true explanation, the hypothesis of the molecular clock is really a tautology, no more than a restatement of the fact that at a molecular level the representatives of any one class are equally isolated from the representatives of another class.

...in other words, to propose two molecular clocks ticking at a different rate, one for the haemoglobin family and one for the cytochrome family. However, as there are hundreds of different families of proteins and each family exhibits its own unique degree of interspecies variation, some greater than haemoglobin, some far less than the cytochromes, then it is necessary to propose not just two clocks but one for each of the several hundred protein families, each ticking and its own unique and highly specific rate. Denton (ETC) Page 296

Looking around a bit, we can go back to the idea of looking for living fossils. That is, extant (present and alive) organisms that also are found in the ancient fossil record. The living fossil provides a means to sample the molecules of an organism that has roots to past geologic time. The lungfish is one such example that Denton discusses in relation to the molecular clock hypothesis and use of molecular data to assess evolution (see Denton (ETC) Pages 301 and 302).

Lungfish almost identical to those of modern Africa are found as fossils in the rocks of the Devonian era 350,000,000 years ago alongside fossils of the earliest amphibians and the very fish groups from which the amphibia supposedly of arose.

In evolutionary terms the lungfish and other living fossils are in a very real sense like samples drawn an eternity ago from near to the main course of the stream of vertebrate life. Denton (ETC) 302

Returning to hemoglobin for a comparison:

Consider the case of the haemoglobin in man and lungfish. Since the two lines are presumed to have diverged in Devonian Times, some four hundred million years ago, the line leading to man has undergone profound physiological and morphological changes, while the modern lungfish is still very close in terms of its morphology and physiology to the ancient fishes. Denton (ETC) Page 303

As above, sequence comparisons yield a pattern of equal distance between vastly different groups of life. So, humans... by the presumed biological evolution... should be exhibiting remarkable morphological transformations and internally considerable organ system development. The molecular 'environment' in such a case must also experience considerable change. Yet the living fossil of today goes back in time to something apparently the same, or nearly so, as the ancient remains indicate by in the fossil record. The lungfish thus is a relatively static organism. It's molecular environment would seem relatively static compared to that of organisms undergoing the rather dramatic transitions, for example, leading to modern humans.

It is very difficult to understand why a protein functioning in the basically unchanging physiological environment of the lungfish's red cell should have undergone precisely the same number of beneficial mutations as a related protein evolving in a line a subject to such global adaptational changes. Denton (ETC) Page 303

Looking back at the pattern revealed for sequences in proteins, Denton notes:

Despite the fact that no convincing explanation of how random evolutionary processes could have resulted in such an ordered pattern of diversity, the idea of uniform rates of evolution is presented in the literature as if it were an empirical discovery. The hold of the evolutionary paradigm is so powerful that an idea which is more like a principle of medieval astrology than a serious twentieth century scientific theory has become a reality for evolutionary biologists.

Here is, perhaps, the most dramatic example of the principle that wherever we find significant empirical discontinuities in nature we invariably face great, if not insurmountable, conceptual problems in envisioning how the gaps could have been bridged in terms of gradual random processes. We saw this in the fossil record, we saw it in the case of the feather, in the case of the avian lung and in the case of the wing of the bat. We saw it again in the case of the origin of life and we see it here in this new area of comparative biochemistry.

What has been revealed as a result of the sequential comparisons of homologous proteins is an order as emphatic as that of the periodic table. Yet in the face of this extraordinary discovery the biological community seems content to offer explanations which are no more than apologetic tautologies. Denton (ETC) Page 306

An Added Thought On Nucleic Acids and the Genetic Code:

For DNA and RNA, there are numerous articles in the recent literature on how similar or dissimilar nucleic acid sequences are between species and within a species experiencing various conditions. The example given above focuses on protein sequences, which in part are a reflection of the genetic code (genome) that determines the amino acid composition of these molecules. One should note that new and unique proteins must come into play to support the increased complexity and functionality of the higher organisms that appear progressively in time. The assumption is that the information in the genome is supplemented to yield these new molecules.

Remember to ask:

Where does this new information come from! Beyond this question, we find another area of discussion is how changes appear in the genome's sequence for various species.

There are also numerous reports about rates of change and clocks in relation to genomes. Researchers sometimes report apparently rapid rates of evolution based on observations of genomes revealing change in relatively short time spans. We might ask how environmental impacts are part of these observed changes. Elsewhere we hint that the rapid change is simply a process that rapidly reveals information already within the standing genome. We hardly hear of such considerations because too often it's evolution that a researcher wants to see in motion.

Further, if a researcher notes a change in 'one direction,' then might this apparent rapid evolutionary trend be reversed later on. And, therefore, will anyone note a rapid return to the former genetic configuration if the environmental conditions change. Our suggestion is simple. If a researcher reveals something that seems in a practical sense too rapid, then why report it merely as evolution in the fast lane? Is this evidence in support of a rate of evolution or a response to outside stimuli. So, in a recent report by the well known researchers who have followed developments and 'evolution' of Darwin's finches on the Galapagos Islands, we see words that do not promise a distinct result. Environment plays a role and maybe, just maybe, the Grants have started with the common presumptions and continued study— 30 years and running for their project— will only reveal what all the other data tell us. There is change, and we might use the word evolution, but it's not the Darwinian type. They entitle their article in Science: " Unpredictable Evolution in a 30-Year Study of Darwin's Finches," (Grant & Grant, Science, Vol 296, Page 707; April 2002), and begin with these words:

Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galapagos island of Daphne Major. ... The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.

By these words, and by everything else that emerges in the window's view, we are not surprised... and yet the Grants need more time... again perhaps to see the theory demonstrated among the oscillations of change in both the species and the environment in which they live. Meanwhile, finches remain finches.


Writer / Editor: Dr. T. Peterson, Director, WindowView.org
(081904)

Quotations from Dr. Michael Denton's "Evolution: A Theory in Crisis" are used by permission of Adler and Adler Publishers Inc., 5530 Wisconsin Ave, Suite 1460, Chevy Chase, MD 20815


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