Homology vs. Darwin

The Types: Why Shared Characteristics Are Bad News for Darwinism
Michael Denton February 29, 2016 3:28 AM 

Editor's note: In his new book Evolution: Still a Theory in Crisis, Michael Denton not only updates the argument from his groundbreaking Evolution: A Theory in Crisis (1985) but also presents a powerful new critique of Darwinian evolution. This article is one in a series in which Dr. Denton summarizes some of the most important points of the new book. For the full story, get your copy of Evolution: Still a Theory in Crisis. For a limited time, you'll enjoy a 30 percent discount at  CreateSpace by using the discount code QBDHMYJH.

One of the major achievements of pre-Darwinian biology was the discovery that the living world is organized into a hierarchy of ever more inclusive classes or Types, each clearly defined by a unique homolog or suite of homologs possessed by all the members of the Type and which in many cases have remained invariant in divergent phylogenetic lines for tens or hundreds of millions of years.

Seeking an explanation for the distinctness of the Types and determining their ontological status was seen to be one of the major tasks of 19th-century biology. Virtually all pre-Darwinian biologists, and many after Darwin, saw the Types as immanent and invariant parts of the world-order, no less than crystals or atoms.

There is currently a widespread impression that pre-Darwinian biologists derived their discontinuous-typological conception of nature from all sorts of discredited metaphysical beliefs. This view has been severely criticized by recent researchers and shown to be largely a myth created by twentieth-century advocates of the neo-Darwinian evolutionary synthesis1 -- what Ron Amundson calls "Synthesis Historiography."2 As Amundson shows, whatever their metaphysical leaning, pre-Darwinian biologists did not derive their view of the Types as changeless components of the world order from any a priori metaphysics but from solid empirical observations.

The 19th-century structuralist conception of the Type, and of an ascending hierarchy of taxa or Types of ever-widening comprehensiveness as immanent features of nature, was close to the classic Aristotelian worldview. But it was based on the facts of biology, not on a philosophical a priori assumption -- Aristotelian, Platonic, or otherwise.

Today, 150 years after Darwin, Owen's "biological atoms" are as distinct as ever. The vast majority of all organisms can be assigned to unique classes based on their possession of particular defining homologs or novelties that are not led up to via Darwin's "innumerable transitional forms."

For readers subjected to popular and pervasive claims by evolutionary biologists that there are innumerable transitional forms of organisms, it might come as something of a surprise that there are unique taxon-defining novelties not led up to gradually from some antecedent form, and that remain invariant after their actualization for vast periods of time.

There is indeed something incongruous about the very notion of distinct taxa and genuine immutable "taxon-defining novelties" in the context of the functionalist Darwinian framework, which implies that all taxa-defining traits should be led up to via long series of adaptive transitional forms! On such a Darwinian model, taxa-defining novelties should not exist; neither should distinct Types in which all members possess unique defining novelties not shared by the members of any other taxa.

Let me reiterate: If evolution has occurred as conceived of by Darwin, invariant taxa-defining novelties, not led up to via long sequences of transitional forms from some antecedent structure, should not exist.

Ironically, it is only because organisms can be classified into distinct groups on the basis of their possession of invariant unique homologs that descent with modification can be inferred in the first place. If it was not for the invariance of the homologs and the Types they define, the common descent of all the members of a particular clade from a common ancestor would be in serious doubt. The living realm would conform to a chaotic network rather than an orderly branching tree.

Types are still as distinct today as they were for Richard Owen, Agassiz, and the other typologists and structuralists in the pre-Darwinian era and even for Darwin himself.3 They are still clearly defined by homologs or synapomorphies that are true evolutionary novelties without antecedent in earlier putative ancestral forms.

References:

(1) Mary Winsor, "The Creation of the Essentialism Story: An Exercise in Metahistory," History and Philosophy of the Life Sciences 28 (2006): 149-174.

(2) Amundson, The Changing Role of the Embryo in Evolutionary Thought, 11.


(3) Charles Darwin, Origin of Species, 6th ed. (London: John Murray 1872), 264 (Chapter 10): "The distinctness of specific forms, and their not being blended together by innumerable transitional links, is a very obvious difficulty."

Another failed Darwinian prediction X

Similar species share similar genes:

The only figure in Darwin’s book, The Origin of Species, showed how he envisioned species branching off of one another. Similar species have a relatively recent common ancestor and have had limited time to diverge from each other. This means that their genes should be similar. Entirely new genes, for instance, would not have enough time to evolve. As François Jacob explained in an influential paper from 1977, “The probability that a functional protein would appear de novo by random association of amino acids is practically zero.” (Jacob) Any newly created gene would have to arise from a duplication and modification of a pre-existing gene. (Zhou et. al.; Ohno) But such a new gene would retain significant similarity to its progenitor gene. Indeed, for decades evolutionists have cited minor genetic differences between similar species as a confirmation of this important prediction. (Berra, 20; Futuyma, 50; Johnson and Raven, 287; Jukes, 120; Mayr, 35)

But this prediction has been falsified as many unexpected genetic differences have been discovered amongst a wide range of allied species. (Pilcher) As much as a third of the genes in a given species may be unique, and even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. (Daubin and Ochman)

Significant genetic differences were also found between different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. (Levine et. al.) As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” (Le Page) These novel genes must have evolved over a few million years, a time period previously considered to allow only for minor genetic changes. (Begun et. al.; Chen et. al., 2007)

Initially some evolutionists thought these surprising results would be resolved when more genomes were analyzed. They predicted that similar copies of these genes would be found in other species. But instead each new genome has revealed yet more novel genes. (Curtis et. al.; Marsden et. al.; Pilcher)

Next evolutionists thought that these rapidly-evolving unique genes must not code for functional or important proteins. But again, many of the unique proteins were in fact found to play essential roles. (Chen, Zhang and Long 1010; Daubin and Ochman; Pilcher) As one researcher explained, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.” (Pilcher)

References

Begun, D., H. Lindfors, A. Kern, C. Jones. 2007. “Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade.” Genetics 176:1131-1137.

Berra, Tim. 1990. Evolution and the Myth of Creationism. Stanford: Stanford University Press.

Chen, S., H. Cheng, D. Barbash, H. Yang. 2007. “Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster.” PLoS Genetics 3.

Chen, S., Y. Zhang, M. Long. 2010. “New Genes in Drosophila Quickly Become Essential.” Science 330:1682-1685.

Curtis, B., et. al. 2012. “Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.” Nature 492:59-65.

Daubin, V., H. Ochman. 2004. “Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli.” Genome Research 14:1036-1042.

Futuyma, Douglas. 1982. Science on Trial: The Case for Evolution. New York: Pantheon Books.

Jacob, François. 1977. “Evolution and tinkering.” Science 196:1161-1166.

Johnson, G., P. Raven. 2004. Biology. New York: Holt, Rinehart and Winston.

Jukes, Thomas. 1983. “Molecular evidence for evolution” in: Scientists Confront Creationism, ed. Laurie Godfrey. New York: W. W. Norton.

Le Page, M. 2008. “Recipes for life: How genes evolve.” New Scientist, November 24.

Levine, M., C. Jones, A. Kern, H. Lindfors, D. Begun. 2006. “Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.” Proceedings of the National Academy of Sciences 103: 9935-9939.

Marsden, R. et. al. 2006. “Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.” Nucleic Acids Research 34:1066-1080.

Mayr, Ernst. 2001. What Evolution Is. New York: Basic Books.

Ohno, Susumu. 1970. Evolution by Gene Duplication. Heidelberg: Springer.

Pilcher, Helen. 2013. “All Alone.” NewScientist January 19.

Zhou, Q., G. Zhang, Y. Zhang, et. al. 2008. “On the origin of new genes in Drosophila.” Genome Research 18:1446-1455.

The first protein vs. Darwin

Yockey and a Calculator Versus Evolutionists

Zero Probability is Not a Problem

In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein. Yockey’s model system was cytochrome c, a protein consisting of about one hundred amino acids. Cytochrome c plays an important role in the mitochondria’s electron transport chain (ETC) which helps to convert the chemical energy in carbon-carbon and carbon-hydrogen bonds, in the food we eat, to an electrochemical potential energy in the form of hydrogen ions (or protons) stored within the mitochondria’s inner membrane. Like water pressing against a dam and turning its turbines to generate electricity, the high-concentration hydrogen ions drive the ATP synthase “turbine” to create the high-energy ATP molecule. Like the electrical outlets in your house, the ATP molecule provides a standardized form of energy that is used for a wide range of applications in your body, such as muscle contraction and nerve signals. There is no scientific explanation for how the ETC evolved. There also is no scientific explanation for how a single protein, such as cytochrome c, evolved. Yockey explained this in 1977, and since then the problem has only gotten worse.

Given 20 different amino acids to choose from, then for a protein with a sequence of 101 amino acids, such as cytochrome c, there are 20 raised to the power of 101, or 20^101, different possible amino acid sequences. That represents an astronomically (and impossible) number of sequences for evolution to search through to find a functional cytochrome c protein.

The problem is more complicated than this, however, since the different amino acids are not equally likely and there are many different sequences that will form a functional cytochrome c protein.

Yockey accounts for these factors to determine the effective number of sequences evolution would have to search through to find cytochrome c. For instance, Yockey uses the known cytochrome c proteins at the time, from many different species, to get an idea of the different amino acids that are possible at each position, within the sequence of 101 residues. Some residues allow for quite a few different amino acids while others seem to be more stringent.

This approach is reasonable, but by no means the only way of estimating the number of different amino acid sequences that could work. One way or another, the bottom line is this: while the number of different sequences that could form a successful type of protein, such as cytochrome c, is a pretty big number, it doesn’t solve the problem.

Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”

Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.

A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.

These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.

Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had. And it assumes the pre existence of bacteria and, yes, proteins. In fact, the evolutionists assumed the earth was covered with bacteria, and each bacteria was full of proteins. That of course is not an appropriate assumption for the question of how proteins could have evolved in the first place. In fact, it is circular.

Of course the evolution of a single protein is only one of many problems for evolution. Consider, for example, the cellular apparatus that constructs proteins—the protein synthesis machinery. One paper used a back-of-the-envelope, simple and conservative calculation to show that the probability of such an apparatus evolving by chance is one in 10^1018. That’s a one followed by 1,018 zeros. Normally in science this would be considered far beyond impossible, so therefore evolutionists are considering an infinite universe, or multiverse, to solve the problem. In such a universe, it does not matter how improbable any event is, it will eventually occur:

Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe … In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.

There you have it. Probabilities don’t matter. You can point out how unlikely evolution is, and evolution remains a fact. Science is done by people, and people seek certain answers, regardless of the data.

Religion drives science, and it matters.

Posted by Cornelius Hunter 

Gilded smoke

Recession proof.

The invincible enemy?:A prequel

Extreme poverty the invincible enemy?

A clash of Titans X

Another failed Darwinian prediction IX

Biology is not lineage specific:

Evolution expects the species to fall into a common descent pattern. Therefore a particular lineage should not have highly differentiated, unique and complex designs, when compared to neighboring species. But this has been increasingly found to be the case, so much so that this pattern now has its own name—lineage-specific biology.

For example, transcription factors are proteins that bind to DNA and regulate which genes are expressed. Yet despite the importance of these proteins, their DNA binding sites vary dramatically across different species. As one report explained, “It was widely assumed that, like the sequences of the genes themselves, these transcription factor binding sites would be highly conserved throughout evolution. However, this turns out not to be the case in mammals.” (Rewiring of gene regulation across 300 million years of evolution) Evolutionists were surprised when transcription factor binding sites were found to be not conserved between mice and men, (Kunarso et. al.) between various other vertebrates, and even between different species of yeast. So now evolution is believed to have performed a massive, lineage-specific “rewiring” of cellular regulatory networks. (Pennacchio and Visel)

There are many more such examples of lineage-specific biology. Although flowers have four basic parts: sepals, petals, stamens and carpels, the daffodil’s trumpet is fundamentally different and must be an evolutionary “novelty.” (Oxford scientists say trumpets in daffodils are ‘new organ’) Out of the thousands of cockroach species, Saltoblattella montistabularis from South Africa is the only one that leaps. With its spring-loaded hind legs it accelerates at 23 g’s and out jumps even grass hoppers. (Picker, Colville and Burrows) An important immune system component, which is highly conserved across the vertebrates, is mysteriously absent in the Atlantic cod, Gadus morhua. (Star, et. al.) The brown algae, Ectocarpus siliculosus, has unique enzymes for biosynthesis and other tasks. (Cock) And the algae Bigelowiella natans has ten thousand unique genes and highly complex gene splicing machinery never before seen in a unicellular organism. It is, as one evolutionist explained, “unprecedented and truly remarkable for a unicellular organism.” (Tiny algae shed light on photosynthesis as a dynamic property)

Another fascinating example of lineage-specific biology are the many peculiar morphological and molecular novelties found in disparate, unrelated unicellular protists. As one study concluded, “Both euglenozoans and alveolates have a reputation for ‘doing things their own way,’ which is to say that they have developed seemingly unique ways to build important cellular structures or carry out molecular tasks critical for their survival. Why such hotspots for the evolution of novel solutions to problems should exist in the tree of life is not entirely clear.” (Lukes, Leander and Keeling, 2009a) Or as one evolutionist exclaimed, “this is totally crazy.” (Lukes, Leander and Keeling, 2009b)

References

Cock, J., et al. 2010. “The Ectocarpus genome and the independent evolution of multicellularity in brown algae.” Nature 465:617-621.

Kunarso G., et. al. 2010. “Transposable elements have rewired the core regulatory network of human embryonic stem cells.” Nature Genetics 42:631-634.

Lukes, J., B. Leander, P. Keeling. 2009. “Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates.” Proceedings of the National Academy of Sciences 106 Suppl 1:9963-9970.

Lukes, J., B. Leander, P. Keeling. 2009. “The corresponding evolutionary histories of euglenozoans and dinoflagellates: cascades of convergent evolution or accumulation of oddities?.” The National Academies. http://sackler.nasmediaonline.org/2009/darwin/julius_lukes/julius_lukes.html

“Oxford scientists say trumpets in daffodils are ‘new organ’.” 2011. BBC News February 28. http://www.bbc.co.uk/news/uk-england-oxfordshire-12598054

Pennacchio, L., A. Visel. 2010. “Limits of sequence and functional conservation.” Nature Genetics 42:557-558.

Picker, M., J. Colville, M. Burrows. 2012. “A cockroach that jumps.” Biology Letters 8:390-392.

“Rewiring of gene regulation across 300 million years of evolution.” 2010. ScienceDaily April 12. http://www.sciencedaily.com/releases/2010/04/100409093211.htm

Star, B., et. al. 2011. “The genome sequence of Atlantic cod reveals a unique immune system.” Nature 477:207–210.

“Tiny algae shed light on photosynthesis as a dynamic property.” 2012. ScienceDaily November 28. http://www.sciencedaily.com­ /releases/2012/11/121128132253.htm

Another failed Darwinian prediction VIII

Serological tests reveal evolutionary relationships:

Early in the twentieth century scientists studied blood immunity and how immune reaction could be used to compare species. The blood studies tended to produce results that parallel the more obvious indicators such as body plan. For example, humans were found to be more closely related to apes than to fish or rabbits. These findings were said to be strong confirmations of evolution. In 1923 H. H. Lane cited this evidence as supporting “the fact of evolution.” (Lane, 47) Later in the century these findings continued to be cited in support of evolution. (Berra, 19; Dodson and Dodson, 65)

But even by mid century contradictions to evolutionary expectations were becoming obvious in serological tests. As J.B.S.Haldane explained in 1949, “Now every species of mammal and bird so far investigated has shown quite a surprising biochemical diversity by serological tests. The antigens concerned seem to be proteins to which polysaccharides are attached.” (quoted in Gagneux and Varki)

Indeed these polysaccharides, or glycans, did not fulfill evolutionary expectations. As one paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” (Bishop and Gagneux) These glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only.

Here is how another paper described glycan findings: “There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages.” (Gagneux and Varki)

References

Berra, Tim. 1990. Evolution and the Myth of Creationism. Stanford: Stanford University Press.

Bishop J., P. Gagneux. 2007. “Evolution of carbohydrate antigens--microbial forces shaping host glycomes?.” Glycobiology 17:23R-34R.

Dodson, Edward, Peter Dodson. 1976. Evolution: Process and Product. New York: D. Van Nostrand Company.

Gagneux, P., A. Varki. 1999. “Evolutionary considerations in relating oligosaccharide diversity to biological function.” Glycobiology 9:747-755.

Lane, H. 1923. Evolution and Christian Faith. Princeton: Princeton University Press.

On the limits of intelligent design theory

Good Questions on the Nature of Intelligent Design
Ann Gauger February 25, 2016 6:01 AM

Earlier, Evolution News responded helpfully to a question from an email correspondent. Here are more questions and answers. A reader writes with a few good queries on the nature of ID theory.

Question:

On the complexity and specificity arguments, I've read that there are two arguments used as evidence for a designer's existence. However, do such arguments entail that the designer is still intervening in the ongoing development of the universe and of life within it? Or does ID only state that there was a designer at least at the very beginning, and ID as a theory does not categorically state (or necessarily entail) that this designer is still interested in making changes? Thus, are the complexity and specificity arguments examples rather than actual requirements?

Answer: ID is about design detection, and makes no statements about ongoing design or a design mechanism. We simply say that there are elements in the universe that give evidence of being designed. Anything further goes beyond what we can say. For example, we can say nothing about how (by what mechanism) design is instantiated. As for specified complexity and irreducible complexity, they are methods of design detection. I see irreducible complexity as a special case of specified complexity. There are probably other valid arguments for design, such as the fact that the universe is intelligible to us when there is no logical requirement that it be so.

Question:

Does ID associate any particular attributes with this "designer"? I am aware that various prominent ID proponents have said, on different occasions, yes and no -- and I do see a difference between a) ID theory itself, and b) personal opinion on aspects of the theory. The first is a necessary contingent on the theory itself. The second is not. My analogy for this is -- Christians believe certain things. Catholics accept the main Christian belief, plus a few other things.

Answer: ID posits nothing about the attributes of this designer, other than the fact that the designer must be capable of carrying out design at the appropriate scale. Anything more is personal opinion. As one leading ID scientist has written:

I myself do believe in a benevolent God, and I recognize that philosophy and theology may be able to extend the argument. But a scientific argument for design in biology does not reach that far. Thus while I argue for design, the question of the identity of the designer is left open. Possible candidates for the role of designer include: the God of Christianity; an angel -- fallen or not; Plato's demiurge; some mystical New Age force; space aliens from Alpha Centauri; time travelers; or some utterly unknown intelligent being. Of course, some of these possibilities may seem more plausible than others based on information from fields other than science. Nonetheless, as regards the identity of the designer, modern ID theory happily echoes Isaac Newton's phrase "Hypothesis non fingo"(I make no hypothesis).

(Michael Behe, "The Modern Intelligent Design Hypothesis," Philosophia Christi, Series 2, Vol. 3, No. 1 (2001), pg. 165)

Question:

Inherent in ID theory, is there the idea that there was purpose in the design? And, if so, what specific purposes?

Answer: ID also does not say anything about purpose, aside from the fact that things, especially biological things, look like they were made to carry out some particular function. They work together as a whole to make a functional organism. That functional organism is part of an ecosystem, and contributes to the functioning of that system. But is there an overall purpose to that system? To make a biosphere? This can be pushed out only so far; as to the reason for the existence of all of this -- why there should be such a planet, or the reason for our existence on the planet -- that goes beyond what ID can say. Final ends belong in the realms of philosophy and theology.

Question:

A personal question regarding how the ID debate has been fought. Why oh why was it based on biology??? IMHO, that was a terrible starting point! I would suggest later iterations and discussions focus on even more fundamental aspects of the universe. Time (apparently) is constant and measurable (not random and chaotic); the universal constant is just that -- a constant -- and without such a very, very limited range of variation, we could not exist (at least, not as we do now). Mathematics works -- again, in my thinking, a sign that this universe is rational; and if rational, designed (rationality and order from chaos...???). I know Plato et al. discussed this, but it seems to have been ignored in the ID debate. As I hope I have clearly indicated, I'm after answers that clearly differentiate ID as a theory in general from any personal takes on it (e.g., characteristics of the designer).

Answer: ID is not based purely on biology, though it may appear to be sometimes. The extreme fine-tuning of the universe for life; the fact that mathematics is rational and elegant, and fits the needs of science; the fact that chemistry is ordered so as to make its discovery possible, and that the planet is ordered so as to permit intelligent life to discover science at all (see The Privileged Planet) -- all these are arguments for design, design that is detectable by minds such as ours. I suggest reading A Meaningful World, by Benjamin Wiker and Jonathan Witt.

The reason it often appears that the argument is all about biology is because it is from there that the majority of pushback comes.


Thanks for your questions, and I hope my response helps.

Darwinism vs, the real world XXXI

The Digestive System: The Stomach and Beyond
Howard Glicksman February 26, 2016 11:24 AM

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series,  see here. Dr. Glicksman practices palliative medicine for a hospice organization.


Except for molecular oxygen (O2), which comes in through the lungs, everything else the body needs to survive enters through the gastrointestinal system. This includes things like water, sugars, amino and fatty acids, cholesterol, electrolytes, minerals, and vitamins. But most of the nutrients the body needs are trapped inside more complex molecules, like carbohydrates, proteins, and fats, and are too large to enter the body. The gastrointestinal system must first break down these large molecules into much smaller ones, in a process called digestion, so it can then absorb the nutrients the body needs into the blood. In my last article I showed that digestion is similar to how a pulp and paper mill works. They both use mechanical and chemical means to break down large things into smaller ones and only use their equipment and chemicals when needed.

The process of digestion begins as soon as food enters the mouth. Its presence, along with its taste and smell, are detected by the nervous system, which stimulates the release of saliva from the glands in the mouth. Saliva contains the enzymes amylase and lipase, which begin the chemical breakdown of carbohydrates and fats respectively. As the food mixes with saliva, it is mashed by the teeth and the tongue, formed into a small mushy lump called a bolus, and moved back toward the pharynx.

Sensors in the pharynx detect the bolus and send information to the brain, initiating the swallow reflex. Swallowing involves the coordinated action of about twenty-five different pairs of muscles to protect the airway and propel the bolus into the esophagus, where it is moved by peristalsis down into the stomach. This article will show how the body follows the rules and takes control to continue digestion and absorption within the stomach and beyond.

Seeing, smelling, and tasting food causes the brain to send nerve messages to the stomach, which begins the first or cephalic phase of gastric secretion. This causes the release of mucous, hydrochloric acid, and pepsinogen. The mucous protects the cells that line the stomach from its own chemicals. The acid both kills microbes and converts pepsinogen into a powerful digestive enzyme called pepsin, a protease that begins to chemically breakdown protein. This phase also results in specialized cells in the stomach secreting a hormone called gastrin,which travels in the blood and tells the stomach cells to send out even more mucous, hydrochloric acid, and pepsinogen.

As the stomach fills up and distends with fluid, the stretch-sensitive mechanoreceptors in its walls send out more nerve messages. These stimulate the cells in the stomach to send out even more mucous, hydrochloric acid, and pepsinogen in what is called the second or gastric phase of gastric secretion. The contents of the stomach are then churned and mixed to further help in the digestive process, creating an acidic liquid called chyme.

It is important to note here that besides playing a major role in digestion, the stomach does two other important things: use its acid to help iron be absorbed later on and produce intrinsic factor to protect Vitamin B12 from being broken down by its acid. Both of these nutrients are needed for the production of hemoglobin.

The stomach absorbs very few nutrients (mainly water) and once it has done its part of digestion it passes the chyme into the first part of the intestine called the duodenum. To prevent damage to the duodenum and allow for more efficient digestion and absorption, it is important that the stomach control how fast it releases the chyme. This is accomplished by the pyloric sphincter, a ring-like band of muscle at the end of the stomach that is able to constrict and relax to send out the right amount of chyme for the right situation. Sensors in this region send messages to nerve cells, which help to control gastric emptying. In general, the more fat and protein is present and the more acidic the chyme, the slower the stomach empties its contents into the duodenum. This is why, when you have a heavier meal, your stomach feels full for a longer period of time.

As the stomach works on the acidic chyme and slowly sends it into the duodenum, the stretching of the intestinal walls signals it to start producing its own fluid. Intestinal juice mainly contains saline (NaCl), mucous, bicarbonate (HCO3-), and digestive enzymes. The alkaline bicarbonate begins to neutralize the acidic chyme that the intestine receives from the stomach. The enzymes produced in the lining of the intestine mainly help to break up the bonds between molecules that contain two sugars. Maltase breaks up the bonds between the two glucose molecules that make up maltose, lactase breaks up the bonds between glucose and galactose which make up lactose, and sucrase breaks up the bonds between glucose and fructose which make up sucrose. The intestine also produces enterokinase, a protease that is important for activating many of the enzymes that come from the pancreas.

As the chyme moves from the stomach into the duodenum, sensors on specialized gland cells detect simple molecules, like fatty and amino acids. The gland cells respond by sending out two hormones, secretin and cholecystokinin, to tell the pancreas to deposit its fluid into the digestive tract. Pancreatic juice contains high amounts of bicarbonate and is very alkaline. The addition of the alkaline pancreatic juice helps to further neutralize the acidic chyme that has entered the intestine from the stomach. The pancreatic juice also contains most of the enzymes needed to finish off the digestion of carbohydrates, fats, and proteins. In addition to amylases and various lipases, the pancreatic juice contains many different proteases that break down proteins. This includes trypsin, chymotrypsins, elastases, and carboxypeptidases. All of these proteases are produced inside the pancreatic cells in the inactive form so they won't digest the pancreas itself.

Trypsin enters the intestine as trypsinogen and becomes activated by its alkaline environment and enterokinase, which, by snipping a few atoms off, changes its shape so it is ready to go to work. Trypsin then activates the other enzymes and proteases, mentioned above. Finally, since lipids are not very soluble in water, they require the presence of bile from the liver and gall bladder to help in fat digestion. The presence of fatty acids in the duodenum contributes to the release of cholecystokinin, which tells the pancreas to release its juice and the gall bladder to contract and send its concentrated bile into the intestine to help in fat digestion.

The intestine, which consists of the duodenum, jejunum, and ileum, is where most of digestion and absorption take place. In addition to water, glucose, amino acids, cholesterol, and simple fats, the intestine also absorbs other vital chemicals, such as minerals, like calcium and iron, electrolytes, like sodium and potassium ions, and vitamins like A, C, D, E, K, and all of the B vitamins, including Vitamin B12. About 1.5 liters of fluid makes its way from the intestine into the colon daily, where mostly water, sodium, and chloride ions are reabsorbed. The remaining 100-150 gm of feces that daily exits the gastrointestinal tract through the rectum and anus usually consists of about 70 percent water and 30 percent solids from undigested plant fibers, like cellulose, cells shed from the lining of the gastrointestinal tract, and bacteria.

A quick review of gastrointestinal function shows that, to do its job properly, it needs separate control systems to turn on different organs, each using enough fluids and chemicals to adequately digest food and absorb enough nutrients. The cephalic and gastric phases of gastric secretion, along with gastrin, make sure the stomach sends out enough acid to activate pepsin for the digestion of proteins to begin. The amount of fatty and amino acids and the acidity of the chyme determine the rate of gastric emptying to help in proper digestion and absorption.

These chemicals also stimulate certain gland cells to release secretin and cholecystokinin, which together tell the pancreas to release its juices into the intestine and the gall bladder to release concentrated bile. Alkaline intestinal and pancreatic juices neutralize the acid coming from the stomach, which, with the help of enterokinase, activates trypsin. Trypsin then activates many other pancreatic enzymes that do most of the work of digestion. Bile from the liver and the gall bladder are needed to help fat digestion as well. Having completed digestion, the intestine then absorbs the nutrients that have been freed up. Finally, the intestine and colon reabsorb most of the water, sodium, and chloride ions that have been previously secreted so that very little is lost through the feces.

The total absence or significant deficiency of any one nutrient would have made it impossible for our earliest ancestors to survive long enough to reproduce. The gastrointestinal system demonstrates irreducible complexity because every component has to be present for it to be able to do its job. It also demonstrates natural survival capacity because each of its components has to provide enough of the right fluid and chemicals to cause adequate digestion and allow for the absorption of what the body needs for survival. Evolutionary biology usually points to similar systems within simpler organisms to explain how the gastrointestinal system may have come into being. Of course, this does not explain how the simpler systems developed in the first place or how it must work within the laws of nature to allow for survival.


The body must breathe in air every few seconds because its need for oxygen is so acute that without it, it dies in just a few minutes. When it comes to water, because the body is able to move some of it from its cells into the blood to compensate for its loss, it only has to drink fluids every few hours. What about glucose? After all, we know we don't have to take in glucose as often as oxygen or water to stay alive. So, how does the body go about making sure it has enough for its energy needs and how does evolutionary biology explain the development of the system it uses? That's what we'll start to look at next time.

As just so as it gets(yet)

New Solution to Darwin's Doubt: Earth Wandered into Cambrian Explosion
Evolution News & Views February 26, 2016 3:14 AM

Since the debut of Darwin's Doubt, we have welcomed all comers to give Darwinian explanations for the Cambrian explosion. We've seen scientists propose a rise in oxygen, the emergence of hard parts, a rise in fecal material, and other creative ideas, including sheer dumb luck. If nothing else, it's entertaining, like watching Britain's Got Talent but, it sometimes seems, a bit light on the talent.

Now there comes along a new solution to the Cambrian enigma, proposed by a team from the University of St. Andrews. The announcement arrives under the promising title, "Unlocking one of the great secrets of Earth's evolution."

They start by making huge promises:

An international team including scientists at the University of St Andrews has unlocked the secret of one of the great events of Earth's evolution -- the Cambrian explosion. [Emphasis added.]
Expectation mounts:

Around 520 million years ago, a wide variety of animals burst onto the evolutionary scene in an event known as the Cambrian explosion. In perhaps as few as 10 million years, marine animals evolved most of the basic body forms that we observe in modern groups.
The event has sparked fierce debate all the way back to Darwin. Some paleontologists see the Cambrian explosion as a real, astonishing episode of unprecedented, fast evolution. Others suggest it is a false artifact of an unreliable fossil record.

The conflict has been established: the realists vs. the artifactualists. It's good to see that this contestant doesn't sidestep the brevity of the record. The team acknowledges that the "unprecedented, fast evolution" occurred in "as few as 10 million years." The alternative, the suggestion of a "false artifact of an unreliable fossil record," leaves much to be desired, since that idea perished quickly after Darwin. The team seems in a bind. Can they pull off a miracle?

Yes! They're going to get the whole planet involved in unlocking the great secret. Here is the main theme:

Now work published in the American Journal of Science shows that these competing theories can be unified by the geography of Cambrian Earth, as it underwent a wholesale lurch that clustered most of Earth's continents around the equator.
Co-author Dr Timothy Raub of the Department of Earth and Environmental Sciences at the University of St Andrews said: "In a nutshell both camps were right. The particular locations of Cambrian continents relative to each other was special in a way that supercharged animal speciation while preserving an unusually good record of those early fossils."

Is this the "lurch" theory of Cambrian animals? OK, you get the continents together; so what? How exactly does that "supercharge speciation"? Fossils can be preserved; great. Fossils of what?

They argue that the Earth lurched about in its orbit so that the continents cluster near the equator. This is dubbed "true polar wander." By chance, the continents created a hothouse ready to nurture the new complex animals.

Earth's continental and oceanic plates are in constant motion relative to one another, but in rare episodes of true polar wander, the entire solid Earth slips about its liquid outer core over the course of five to ten millions years, causing the geographic locations of Earth's plates to shift altogether in the same sense.
The paper suggests that about 520 million years ago a lurch of more than 60 degrees moved most continents from polar to tropical latitudes. For reasons that are still debated, biological diversity reaches a global peak around the equator and tapers off closer to the poles. This early Cambrian rotation therefore would have dramatically increased shallow coastal area in Earth's biodiversity hotspot.

Then, they say, a great bulge of water swamped continental coastlines, burying organisms under floods of sediment. The setting "would have opened up new habitats for rapid diversification, in particular vast continental seaways rife with previously unexplored ecological niches" and then preserving whatever, well -- whatever took advantage of the habitats.

That rather awkward ending deserves to be greeted with courtesy applause. One imagines Simon Cowell responding, "Thank you for that, but I do have a question; I'm a little confused where the animal body plans come from. You've set the table for them, surely; you've provided them with a nice hothouse and some unexplored habitats, but isn't the challenge how to explain the animals themselves?"

They never really grapple with the problem of new body plans, settling for vague language:

Cambrian true polar wander happened at a time when Earth was already seeded with many of the traits that subsequently radiated throughout the Tree of Life.
If one of us were a judge on this imaginary competition, the dialogue might go something like this: "I see, but...seeds? Are you saying that simple Ediacaran animals planted trilobite seeds and worm seeds and jellyfish seeds? I'm not sure I follow this line."

Dr Raub said: "A bunch of wonderful ideas have been published emphasising one or another aspect of the Cambrian biosphere as the crucial link in the explosion of animal life. An appealing aspect of our study is that a geographic contingency -- the shape and arrangement of the Cambrian continents and the direction of the remarkable true polar wander shift -- can support almost all those ideas simultaneously. At the same time, it turns out that preservation of Cambrian fossils really was enhanced over that of other ages....
Another judge chimes in: "Geographic contingency...are you telling us that it happened by chance? We were hoping to hear you explain the origin of nearly twenty unique animal body plans through a plausible biological mechanism in a very short period of time."

Another judge: "You can't fossilize what doesn't exist. Even if the continents lined up near the equator like you say, there should have only been Ediacaran organisms at the time. Where did the information come from to build all those body plans?"

They really haven't addressed the main issue. What could this presentation possibly do to, as they claim, "unlock the secret" of the Cambrian explosion?

"This new geographic framework answers a debate going back over a hundred years. It should encourage scientists to review all sorts of old and new hypotheses, which no longer must fit into the evolution or preservation camp exclusively."
The uncomfortable exchange continues: "You mean, like the intelligent design camp perhaps?" With a shocked expression, he responds, Well, no; of course not. Cowell continues, "Doesn't that qualify for inclusion in "all sorts of old and new hypotheses?" The respondent gulps. I thought we were talking scientific hypotheses. "So contingency is a scientific hypothesis?" Well, no, but... "Where did the information come from to build twenty new animal body plans?" Our model wasn't concerned with that, but rather with how the continents became rearranged to make whatever happened possible.


Thank you for your time. Next.

The Watchtower Society's commentary on the book of Habakkuk.

HABAKKUK, BOOK OF;

A book of the Hebrew Scriptures in eighth place among the so-called minor prophets in the Hebrew and Septuagint texts, as well as in common English Bibles. It is in two parts: (1) A dialogue between the writer and Jehovah (chaps 1, 2); (2) a prayer in dirges.—Chap 3.

Writer. The writer is identified in the book itself. The composition of both sections is ascribed to “Habakkuk the prophet.”—1:1; 3:1; see HABAKKUK.

Canonicity. The canonicity of the book of Habakkuk is confirmed by ancient catalogs of the Hebrew Scriptures. While they do not mention it by name, the book evidently was embraced by their references to the ‘twelve Minor Prophets,’ for otherwise the number 12 would be incomplete. The book’s canonicity is unquestionably supported by quotations from it in the Christian Greek Scriptures. Though not referring to Habakkuk by name, Paul quoted Habakkuk 1:5 (LXX) while speaking to faithless Jews. (Ac 13:40, 41) He quoted from Habakkuk 2:4 (“But as for the righteous one, by his faithfulness he will keep living”) when encouraging Christians to display faith.—Ro 1:16, 17; Ga 3:11; Heb 10:38, 39.

Among the Dead Sea Scrolls is a manuscript of Habakkuk (chaps 1, 2) in a pre-Masoretic Hebrew text with an accompanying commentary. It is noteworthy that in the text Jehovah’s name is written in ancient Hebrew characters, whereas in the commentary the divine name is avoided, and instead, the Hebrew word ʼEl (meaning “God”) is used.

Scholars believe that this scroll was written toward the end of the first century B.C.E. This makes it the oldest extant Hebrew manuscript of the book of Habakkuk. At Habakkuk 1:6 this manuscript reads “Chaldeans,” thus confirming the correctness of the Masoretic text in showing that the Chaldeans (Babylonians) were the ones Jehovah would raise up as his agency.

Date and Setting. The statement “Jehovah is in his holy temple” (Hab 2:20) and the note that follows Habakkuk 3:19 (“To the director on my stringed instruments”) indicate that Habakkuk prophesied before the temple built by Solomon in Jerusalem was destroyed in 607 B.C.E. Also, Jehovah’s declaration “I am raising up the Chaldeans” (1:6) and the prophecy’s general tenor show that the Chaldeans, or Babylonians, had not yet desolated Jerusalem. But Habakkuk 1:17 may suggest that they had already begun to overthrow some nations. During the reign of Judah’s good king Josiah (659-629 B.C.E.), the Chaldeans and Medes took Nineveh (in 632 B.C.E.), and Babylon was then on its way toward becoming a world power.—Na 3:7.

There are some who hold, in agreement with rabbinic tradition, that Habakkuk prophesied earlier, during the reign of King Manasseh of Judah. They believe that he was one of the prophets mentioned or alluded to at 2 Kings 21:10 and 2 Chronicles 33:10. They hold that the Babylonians were not yet a menace, which fact made Habakkuk’s prophecy more unbelievable to the Judeans.—See Hab 1:5, 6.

On the other hand, in the early part of Jehoiakim’s reign, Judah was within the Egyptian sphere of influence (2Ki 23:34, 35), and this could also be a time when God’s raising up of the Chaldeans to punish the wayward inhabitants of Judah would be to them ‘an activity they would not believe, though it was related.’ (Hab 1:5, 6) Babylonian King Nebuchadnezzar defeated Pharaoh Necho at Carchemish in 625 B.C.E., in the fourth year of King Jehoiakim’s reign. (Jer 46:2) So, Habakkuk may have prophesied and recorded the prophecy before that event, possibly completing the writing thereof about 628 B.C.E. in Judah. The use of the future tense regarding the Chaldean threat evidently indicates a date earlier than Jehoiakim’s vassalship to Babylon (620-618 B.C.E.).—2Ki 24:1.

Style. The style of writing is both forceful and moving. Vivid illustrations and comparisons are employed. (Hab 1:8, 11, 14, 15; 2:5, 11, 14, 16, 17; 3:6, 8-11) Commenting on Habakkuk’s style, S. R. Driver said: “The literary power of Habakkuk is considerable. Though his book is a brief one, it is full of force; his descriptions are graphic and powerful; thought and expression are alike poetic.” Such qualities are, of course, primarily due to divine inspiration.

The book of Habakkuk emphasizes Jehovah’s supremacy over all nations (Hab 2:20; 3:6, 12), highlighting his universal sovereignty. It also places emphasis on the fact that the righteous live by faith. (2:4) It engenders reliance upon Jehovah, showing that he does not die (1:12), that he justly threshes the nations, and that he goes forth for the salvation of his people. (3:12, 13) For those exulting in him, Jehovah is shown to be the God of salvation and the Source of vital energy.—3:18, 19.

[Box on page 1013]

HIGHLIGHTS OF HABAKKUK

An answer to the question, Will God execute the wicked?

Written evidently about 628 B.C.E., when the Chaldeans were rising in prominence but before Jehoiakim became their vassal

Habakkuk cries out for help, asks how long God will allow the wicked to continue (1:1–2:1)

When Jehovah answers that He will raise up the Chaldeans as His instrument for punishment, Habakkuk cannot understand how the Holy One could countenance such a treacherous agent, one who makes a god of his war machine, whose dragnet gathers up men like fish, and who mercilessly kills peoples

The prophet waits for Jehovah’s answer, recognizing that he is in line for reproof

Jehovah replies that he has an appointed time, pronounces woe upon the Chaldean agency (2:2-20)

Jehovah gives the assurance that even though there might seem to be delay, the prophetic vision is “for the appointed time, and it keeps panting on to the end,” eagerly moving toward its fulfillment

Pronouncements of woe indicate that the Chaldean instrumentality would not remain unpunished for plundering other nations, cutting off many peoples, building cities by bloodshed, making others drink the cup of shameful defeat, and engaging in idolatry

The prophet appeals for Jehovah to act and yet to show mercy during the coming day of distress (3:1-19)

Recalling past manifestations of Jehovah’s power, the prophet is seized with fear and trembling, but he is determined to wait quietly for the day of distress, exulting in the God of his salvation


Even if the very means for supporting life were to fail, Habakkuk determines to rejoice in Jehovah as the God of salvation, the One who strengthens him

Darwinists brainstorm yet another just so story.

How to Build Life in a Pre-Darwinian World:
By: Emily Singer


How did life’s myriad parts come together? At a minimum, the first life forms on Earth needed a way to store information and replicate. Only then could they make copies of themselves and spread across the world.One of the most influential hypotheses states that it all began with RNA, a molecule that can both record genetic blueprints and trigger chemical reactions. The “RNA world” hypothesis comes in many forms, but the most traditional holds that life started with the formation of an RNA molecule capable of replicating itself. Its descendants evolved the ability to perform an array of tasks, such as making new compounds and storing energy. In time, complex life followed.

However, scientists have found it surprisingly challenging to create self-replicating RNA in the lab. Researchers have had some success, but the candidate molecules they have manufactured to date can only replicate certain sequences or a certain length of RNA. Moreover, these RNA molecules are themselves quite complicated, raising the question of how they might have formed through chance chemical means.

Nick Hud, a chemist at the Georgia Institute of Technology, and his collaborators are looking beyond biology to the role of chemistry in the development of life. Perhaps before biology arose, there was a preliminary stage of proto-life, in which chemical processes alone created a smorgasbord of RNAs or RNA-like molecules. “I think there were a lot of steps before you get to a self-replicating self-sustaining system,” Hud said.

In this scenario, a variety of RNA-like molecules could form spontaneously, helping the chemical pool to simultaneously invent many of the parts needed for life to emerge. Proto-life forms experimented with primitive molecular machinery, sharing their parts. The entire system worked like a giant community swap meet. Only once this system was established could a self-replicating RNA emerge.At the heart of Hud’s proposal is a chemical means for generating a rich diversity of proto-life. Computer simulations show that certain chemical conditions can produce a varied collection of RNA-like molecules. And the team is currently testing the idea with real molecules in the lab; they hope to publish the results soon.

Hud’s group is leading the way for a number of researchers who are challenging the traditional RNA-world hypothesis and its reliance on biological rather than chemical evolution. In the traditional model, new molecular machinery was created using biological catalysts, known as enzymes, as is the case in modern cells. In Hud’s proto-life stage, myriad RNA or RNA-like molecules could form and change through purely chemical means. “Chemical evolution could have helped life get started without enzymes,” Hud said.

Hud and his collaborators have taken this idea one step further, suggesting that the ribosome, the only piece of biological machinery that is found in all living things today, emerged through chemistry alone. That’s an unconventional thought to many in the field, who think that the ribosome was born of biology.

If Hud’s team can create proto-life forms under conditions that might have existed on the early Earth, it would suggest that chemical evolution may have played a much more significant role in the origins of life than scientists expected. “Maybe there was some simpler form of evolution that preceded Darwinian evolution,” said Niles Lehman, a biochemist at Portland State University in Oregon.

The Pre-Darwinian World

When most people think about evolution, they think about Darwinian evolution, in which organisms compete with one another for limited resources and pass on genetic information to their offspring. Each generation undergoes genetic tweaks, and the most successful progeny survive to pass along their own genes. That mode of evolution dominates life today.

Carl Woese, a renowned biologist who gave us the modern tree of life, believed that the Darwinian era was preceded by an early phase of life governed by very different evolutionary forces. Woese thought it would have been nearly impossible for an individual cell to spontaneously come up with everything it needed for life. So he envisioned a rich diversity of molecules engaged in a communal existence. Rather than competing with each other, primitive cells shared the molecular innovations they invented. Together, the pre-Darwinian pool created the components needed for complex life, priming the early Earth for the emergence of the magnificent menagerie we see today.

Hud’s model takes Woese’s pre-Darwinian vision even further back in time, providing a chemical means for producing the molecular diversity that primitive cells needed. One proto-life form might have developed a way to make the building blocks it needed to make more of itself, while another might have found a way to harvest energy. The model differs from the traditional RNA-world hypothesis in its reliance on chemical rather than biological evolution.

According to RNA world, the first RNA molecules replicated themselves using a built-in enzyme called a ribozyme that was made of RNA. In Hud’s proto-life world, that task is accomplished through purely chemical means. The story begins with a chemical soup of RNA-like molecules. Most of these would have been short, as short strands are more likely to form spontaneously, but a few longer, more complex molecules might have come together as well. Hud’s model describes how the longer molecules might have replicated without the aid of an enzyme.In Hud’s vision of a prebiotic world, the primordial RNA soup underwent regular cycles of heating and cooling in a thick, viscous solution. Heat separated the bound pairs of RNA, and the viscous solution kept the separated molecules apart for a while. In the interim, small segments of RNA, just a few letters in length, stuck to each long strand. The small segments eventually got sewn together, forming a new strand of RNA that matched the original long strand. The cycle then began again.

Over time, a pool of varied RNA-like molecules would have accumulated, some of them capable of simple functions, such as metabolism. And just like that, purely chemical reactions would have produced the molecular diversity needed to create Woese’s pre-Darwinian cornucopia of proto-life.

Hud’s team has been able to carry out the first stages of the replication process in the laboratory, although they can’t yet glue together the short segments without resorting to biological tools. If they can get over that hurdle, they’ll have created a versatile way of replicating any RNA that pops up.

Yet some scientists are skeptical that chemically mediated replication could work well enough to produce the pre-Darwinian world Hud describes. “I don’t know whether I believe it,” said Paul Higgs, a biophysicist at McMaster University in Hamilton, Ontario, who studies the origins of life. “It would have to be sufficiently accurate and rapid to pass on the sequence” — that is, it would need to produce new RNAs more quickly than they broke down and with enough fidelity to create near copies of the template molecule.Chemical change on its own wouldn’t have been enough to trigger the emergence of life. The pool of proto-life would also have needed some kind of selection to make sure that useful molecules succeeded and multiplied. In their model, Hud’s team proposes that very simple proto-enzymes might have spread if they did something helpful for their maker and the larger community. For example, an RNA molecule that made more of its own building blocks would benefit itself and its neighbors by providing additional raw materials for replication. In computer simulations that Hud’s team performed, this type of molecule did indeed take root. “If a sequence comes along that does something useful, it can then be enriched in the pool,” Hud said.

Ribosomal Roots

One possible glimpse of the pre-Darwinian world can be seen in the ribosome, an ancient piece of molecular machinery that lies at the heart of our genetic code. It is an enzyme that translates RNA, which encodes genetic information, into proteins, which carry out the many chemical reactions in our cells.

The core of the ribosome is made of RNA. This feature makes the ribosome unique — the vast majority of enzymes in our cells are made from proteins. Both the ribosomal core and the genetic code are shared among all living things, suggesting that they were present very early in the evolution of life, perhaps before it crossed the Darwinian threshold.

Related Articles:

Chemists Seek Possible Precursor to RNA
Scientists have discovered building blocks similar to those in modern RNA that can effortlessly assemble when mixed in water and heated.

New Twist Found in the Story of Life’s Start
All life on Earth is made of molecules that twist in the same direction. New research reveals that this may not always have been so.

How Structure Arose in the Primordial Soup
Life’s first epoch saw incredible advances — cells, metabolism and DNA, to name a few. Researchers are resurrecting ancient proteins to illuminate the biological dark ages.

Hud and his collaborator Loren Williams, also at Georgia Tech, point to the ribosome as support for their chemically dominated world. In a paper published last year, they made the controversial proposal that the core of the ribosome was created via chemical evolution. They also suggested that it arose before the first self-replicating RNA molecule. Perhaps the ribosomal core was a successful experiment in chemical evolution, they said. And after it took root in the pre-Darwinian soup, it crossed the Darwinian threshold and became an essential part of all life.

Their argument centers on the relative simplicity of the ribosomal core, more formally known as the peptidyl transferase center (PTC). The PTC’s job is to bring together amino acids, the building blocks of proteins. Unlike traditional enzymes, which speed up chemical reactions by using “fancy chemical tricks,” as Lehman put it, it works almost like a dehydrator. It coaxes two amino acids to bond simply by removing a molecule of water. “It’s kind of a poor way to drive a reaction,” Lehman said. “Protein enzymes typically rely on more powerful chemical strategies.”

Lehman notes that simplicity likely preceded power in the earliest stages of life. “When thinking about the origins of life, you have to think about simple chemistry first; any process with simple chemistry is probably going to be ancient,” he said. “I think that’s more powerful evidence than the fact that it’s [shared] among all life.”

Despite the powerful evidence, it’s still hard to imagine how the ribosomal core could have been created by chemical evolution. An enzyme that makes more of itself — like the replicator RNA of the RNA-world hypothesis — automatically creates a feedback loop, continually boosting its own production. By contrast, the ribosomal core doesn’t produce more ribosomal cores. It produces random chains of amino acids. It’s unclear how this process would encourage the production of more ribosomes. “Why would making random peptides make that thing better?” Higgs said.

Hud and his collaborators propose that RNA and proteins evolved in tandem, and those that figured out how to work together survived best. This idea lacks the simplicity of the RNA world, which posits a single molecule capable of both encoding information and catalyzing chemical reactions. But Hud suggests that facility might trump elegance in the emergence of life. “I think there’s been an overemphasis on what we call simplicity, that one polymer is simpler than two,” he said. “Maybe it’s easier to get certain reactions going if two polymers work together. Maybe it’s simpler for polymers to work together from the start.”

This article was reprinted on TheAtlantic.com.

The crisis continues. II

Conversations with Dr. Denton: The Hierarchy of Nature
David Klinghoffer February 24, 2016 4:13 AM