Waiting for the other shoe to drop?

Homochirality: The Truth Is Out Where?
Evolution News & Views January 31, 2011 7:00 AM

When it comes to origin of life scenarios, the only way to explain the emergence of life from purely naturalistic premises is that life, and all of its necessary components, arose by chance, or by natural laws or by some combination of both.

Whether life arose in a "warm little pond" or in heat vents or in ice crystals, origin of life scenarios must rely only on chance and natural laws (chemical and physical properties) to explain seemingly impossible phenomenon, such as how DNA first arose.

Right-handed amino acids are found in nature, but for whatever reason proteins only employ left-handed amino acids. Laboratory synthesis of amino acids produces a 50/50 mixture, as is expected with chiral molecules, and both are chemically equivalent. Obviously this cannot be attributed to chance any more so than someone flipping a coin 100 times and getting all heads can. So from naturalistic premises, the only way to solve this is to find some reason why the chemistry favored a particular orientation of biomolecules.

One piece of the origin of life puzzle is that biological molecules have a particular chemical orientation. Biological molecules are composed of carbon, and carbon can form four bonds. When there are different things coming off of those four bonds, it makes a difference where those bonds are with respect to each other. For example, when you look at your hands, your thumb could come off of the right side of the hand or the left side of the hand. The orientation of your thumb and fingers relative to each other makes a difference. Your hands are not superimposable (the same); they are mirror images. Carbon bonds have a similar characteristic. When a carbon-containing molecule has a bond structure around a carbon such that if the bonds were arranged differently the molecules would not be superimposible, it is said to be a chiral carbon or a chiral molecule (from the Greek for "hand"). An interesting thing about chirality is that it does not change the chemical nature of the carbon bonds. So if you have a reaction that ends up making a chiral carbon, you will probably get a 50/50 mixture of left- and right-handed molecules.

All of the amino acids, except glycine, have a chiral carbon. Here is the rub: Amino acids that are from naturally occurring proteins are all left-handed.

The two pervading naturalistic theories on this are: 1) Evolution selected left-handed biomolecules or 2) they were formed in outer space. The exact mechanism for these two theories is the fuel for research and publications. Recently, the Astrophysical Journal published a paper that studies ultra-violet circularly polarized light because this is one of the few ways that can produce a particular handedness (e.g. more right-handed molecules than left-handed molecules) in organic molecules (The Astrophysical Journal Letters, 727:L27, February 2011). Since the mirror images of chiral molecules are called enantiomers, a mixture that has more than 50% of one enantiomer over is another is said to have an enantiomeric excess (e.e.).

Some primitive meteorites contain a small enantiomeric excess of certain chiral amino acids, leading many people to believe that perhaps the origin of homochirality is found in outer space. The authors of the Astrophysical Journal paper sought to investigate what kind of cosmic phenomenon would cause this. One possibility is UV-circularly polarized light (UV-CPL) acting on cosmic "ices" or chunks of cold rock that eventually become meteors. "...we tested such a scenario in a laboratory simulation using UV-CPL to drive the photochemistry of cosmic ice analogs under plausible astrophysical conditions and search for the generation of chiral species with significant e.e.'s..."
They decided to compare their experiments to the Murchison Meteorite, which landed in Australia on September 28, 1969 (Garrett & Grisham Biochemistry 2nd Ed, Harcourt, Inc, 1999). This meteorite showed an enantiomeric excess of several amino acids of 2-9%. The authors looked at alanine, which had an enantiomeric excess of 1.2% on the Murchison Meteorite.

For the experiment, the authors selected a particular photon energy that they knew was close to the maximum needed for alpha hydrogenated amino acids, and directed those photons to a synthesized ice mixture that is theoretically similar to cosmic ice mixtures. To simulate interstellar conditions, they used ice mixtures of the composition H2O:CH3OH:NH3 (2:1:1).

This experiment resulted in a 1.34% e.e. of left-handed alanine, close to the 1.2% reported for the Murchison Meteorite. Other amino acids of interest were too dilute to take meaningful measurements. Usually with these syntheses the smallest amino acids are formed in greater amounts. Alanine is the smallest chiral amino acid. The authors' assumptions are first, amino acids formed in outer space under similar conditions to what they have reconstructed in the lab, and secondly, that these molecules were exposed to UV-CPL under the appropriate conditions to cause an enantiomeric excess of left-handed amino acids.

A couple of experimental procedural notes:

First, to get the laboratory experiment to work, the UV-CPL radiation temperature was increased to higher levels than what is thought to be in outer space, but the authors explain that this is still reasonable since the meteor will likely go through various temperatures: "The use of a higher temperature (80 K), rather than observed temperatures for interstellar ices (10-20 K), was decided to enhance diffusivity and recombination of photoproducts within the ices...However, since the complete cycle of inter and circumstellar grain evolution comprises cycles through warmer regions (hot cores) in which grain temperatures rise significantly (200 K), astronomical organic residues should be produced via pathways similar to those in our laboratory simulations." The authors justify this by referencing experimental studies that showed irradiation temperature (10 or 80 K) does not greatly influence product composition.

Second, they chose to irradiate for 10 hr with the molecules at room temperature (this would be about 20 C or 293 K) "to potentially favor enantioselective photoreactions based on a photon-molecule asymmetry transfer..." In other words, they shot photons at the compounds for a particular amount of time at a particular temperature that they knew would favor the reactions they were pursuing. The authors still contend that this remains astrophysically relevant particularly in "hot molecular core environments, where grains are heated and complex gas-phase molecules, thermally desorbed from the ices, are observed..."

While the authors may have a point that there are hot cores in outer space, they are adding an additional factor by assuming that the meteor must apparently pass through a hot core for a period of time and under certain conditions. At this point, there has been quite a bit of experimenter intervention for what they consider a "natural" process.

A 1.34% enantiomeric excess is significant enough to measure, but does this experiment solve the mystery behind homochirality? Let's consider what is most reasonable and probable. Obviously scientists are looking for an explanation for homochirality because the chances of nature accidentally selecting left-handed amino acids in a pool of a 50/50 mix are impossible. So, instead, the possibility presented here supposes that a meteor somehow went through a heat core and was exposed, apparently within the heat core, to UV-CPL with particular helical properties ended up with some amino acids with a slight e.e. on it. It hit the earth, and happened to hit in such a way that the amino acids were not destroyed upon entry, which is possible given the Murchison Meteorite, but then landed in a place conducive for reactions to take place. Furthermore, the authors mention that other amino acids on the Murchison Meteorite show a greater e.e for molecules such as isovalene "that cannot be explained solely by the asymmetric effect of UV-CPL," meaning that the meteor had to have gone through yet another process to produce the enantiomeric excess of other amino acids. Then those reactions apparently beginning with anywhere from 1.2 to 9% e.e. of left-handed amino acids ended up producing 100% e.e. of the chiral amino acids, which is still inexplicable. How is this any more probable than nature just happening to find the one place where a 50/50 racemic mixture was not made and chemistry did not behave as it normally would? 


This paper is interesting because it may account for the 1.2% e.e. of L-alanine in the Murchison Meteorite, although even this is questionable since their procedure does not account for the other amino acids on the meteorite. However, it does not offer much by way of explaining this very difficult origin of life puzzle. The final section of the paper speculates on where UV-CPL sources of the particular helical value necessary for hydrolyzed amino acids might be found. They suggest this type of UV-CPL was "most probably produced by dichroic scattering [ref removed] on aligned grains by a magnetic field in reflection nebulae close to regions containing massive stars." They speculate that this might be similar to where the Sun was formed. By continuing to add specific conditions upon specific conditions, the likelihood that a meteor brought left-handed amino acids to earth which lead to the subsequent beginning of life is quickly diminishing.

Isaiah Ch.3 NASB

1For behold, the Lord GOD of hosts is going to remove from Jerusalem and Judah
            Both supply and support, the whole supply of bread
            And the whole supply of water;
      2The mighty man and the warrior,
            The judge and the prophet,
            The diviner and the elder,      3The captain of fifty and the honorable man,
            The counselor and the expert artisan,
            And the skillful enchanter.      4And I will make mere lads their princes,
            And capricious children will rule over them,      5And the people will be oppressed,
            Each one by another, and each one by his neighbor;
            The youth will storm against the elder
            And the inferior against the honorable.      6When a man lays hold of his brother in his father’s house, saying,
            “You have a cloak, you shall be our ruler,
            And these ruins will be under your charge,”      7He will protest on that day, saying,
            “I will not be your healer,
            For in my house there is neither bread nor cloak;
            You should not appoint me ruler of the people.”      8For Jerusalem has stumbled and Judah has fallen,
            Because their speech and their actions are against the LORD,
            To rebel against His glorious presence.      9The expression of their faces bears witness against them,
            And they display their sin like Sodom;
            They do not even conceal it.
            Woe to them!
            For they have brought evil on themselves.      10Say to the righteous that it will go well with them,
            For they will eat the fruit of their actions.      11Woe to the wicked! It will go badly with him,
            For what he deserves will be done to him.      12O My people! Their oppressors are children,
            And women rule over them.
            O My people! Those who guide you lead you astray
            And confuse the direction of your paths.
God Will Judge
13The LORD arises to contend,
            And stands to judge the people.      14The LORD enters into judgment with the elders and princes of His people,
            “It is you who have devoured the vineyard;
            The plunder of the poor is in your houses.      15“What do you mean by crushing My people
            And grinding the face of the poor?”
            Declares the Lord GOD of hosts.
Judah’s Women Denounced
16Moreover, the LORD said, “Because the daughters of Zion are proud
            And walk with heads held high and seductive eyes,
            And go along with mincing steps
            And tinkle the bangles on their feet,      17Therefore the Lord will afflict the scalp of the daughters of Zion with scabs,
            And the LORD will make their foreheads bare.”18In that day the Lord will take away the beauty of their anklets, headbands, crescent ornaments, 19dangling earrings, bracelets, veils, 20headdresses, ankle chains, sashes, perfume boxes, amulets, 21finger rings, nose rings, 22festal robes, outer tunics, cloaks, money purses, 23hand mirrors, undergarments, turbans and veils.      24Now it will come about that instead of sweet perfume there will be putrefaction;
            Instead of a belt, a rope;
            Instead of well-set hair, a plucked-out scalp;
            Instead of fine clothes, a donning of sackcloth;
            And branding instead of beauty.      25Your men will fall by the sword
            And your mighty ones in battle.      26And her gates will lament and mourn,
            And deserted she will sit on the ground.

universal common ancestry in the hotseat IV

The Naked Ape: An Open Letter to BioLogos on the Genetic Evidence, Cont.
Cornelius Hunter

In a previous article I reviewed BioLogos Fellow Dennis Venema's articles (here and here) which claimed that the genomes of different species are what we would expect if they evolved. For instance, allied species have similar genomes, and genetic features fall into evolution's common descent pattern. I argued that this claim is inaccurate and that the scientific evidence tells a very different message.
In a later article Venema focused his claim on the specific case of human evolution, and the similarity between the human and chimpanzee genomes. As before, Venema finds this genetic evidence to be a compelling confirmation of evolution:

The first line of evidence in favor of humans sharing ancestry with other forms of life is straightforward -- there are other species that have a genome that is nearly identical to our own -- the genomes found in great apes such as chimpanzees, gorillas and orangutans. Compared to our "book," the "books" of these species match at the chapter and paragraph level -- all three species have DNA sequences that have the same genes in the same basic order as we do. There are subtle differences, of course -- blocks of sequence that have been rearranged through breakage and rejoining of chromosomes, as expected -- but the overall pattern is clear.
...
Taken together, what we observe when comparing the overall structure of the human genome to other primates is that (a) our genomes do indeed have the features one would predict them to have if they are copies of a shared ancestral genome, and (b) the differences we do observe are easily accounted for by well-known mechanisms. These observations strongly support the hypothesis that our species arose through an evolutionary process.

It does not seem that the evidence supports evolutionary theory as Venema concludes. In fact, there appear to be several significant problems with this claim, as I will explain.
First, as we saw in my previous article, the genetic data from the different species do not fall into the expected evolutionary pattern. Here Venema focuses on the high genetic similarity between the primates, claiming it confirms evolution. But if this is what is required to confirm evolutionary relationships, then the substantial genetic differences that are so often found between otherwise similar species must falsify evolutionary relationships in those cases.
But evolutionists have never entertained any such doubts. Those evolutionary relationships are intact, according to evolutionists, and this suggests that the high similarity between the primate genomes never was required for evolutionists to believe they evolved from a common ancestor.
So it appears that Venema's claim, that the high genetic similarity between the primates confirms their evolutionary relationship, is more of an "after the fact" claim rather than a confirmation of a genuine evolutionary prediction. In fact, given the substantial morphological differences between humans and the other primates, evolutionists had indeed expected greater genetic differences:

The chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small.

So it does not appear that the high similarity between the chimp and human genomes was predicted by evolution, or is required by evolution. Beyond that, given the high similarity between the chimp and human genomes, there are many inconsistencies with evolution, as we shall see next.
The Gorilla Genome Is Strangely Similar to Both the Chimp and Human Genomes
When the human and chimpanzee genomes were compared a few years ago, the human genes showed some surprising differences in a few places, such as in genes thought to be related to hearing. Evolutionists called it "accelerated" evolution and they said that it was due to the development of human language. However it turns out that the gorilla genome has a similar pattern. And that doesn't make sense since gorillas don't have our advanced verbal skills:

Much of the 15% is in sections of the genome that do not code for proteins. But the researchers also looked at functional gene changes. They found that certain genes -- including some involved in hearing and brain development -- had gone through more rapid changes than expected in both the gorilla and human lineage. Some of these rapid changes are puzzling: the gene LOXHD1 is involved in hearing in humans and was therefore thought to be involved in speech, but the gene shows just as much accelerated evolution in the gorilla. "But we know gorillas don't talk to each other--if they do they're managing to keep it secret," says [lead author] Scally.

So now evolutionists are calling it "parallel accelerated" evolution, because the same accelerated evolution, by random mutation, must have happened independently, in the human and gorilla genomes. But why would the same "accelerated evolution" occur in the gorilla? It wasn't developing human language. Perhaps there is some other reason, but why then wouldn't that "accelerated evolution" occur in the chimpanzee? It doesn't make sense with evolution, for we must say that random mutations just happened to create the same pattern twice.
The gorilla genome also shows similarities to the chimp genome, including duplications that are not present in the other primates. Evolutionists say these various chimp-gorilla similarities were coincidences, occurring repeatedly by chance in the two different species:

We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations.

These events must have occurred independently and in parallel.
Viruses
Human uniqueness is expansive. Relative brain size, hairless sweaty skin, striding bipedal posture, long-distance running, ability to learn to swim, innate ability to learn languages in childhood, prolonged helplessness of the young, ability to imitate and learn, inter-generational transfer of complex cultures, awareness of self and of the past and future, theory of mind, increased longevity, provisioning by post-menopausal females, difficult childbirth, and cerebral cortical asymmetry are just a few from a long list of features that make humans exceptional.
Another such unique feature is at the genome level: the lack of endemic infectious retroviruses in humans. The problem is that these viruses are present in the other primates, and so according to evolution these viruses must be present in their common ancestor which, again according to evolution, would be an ancestor of humans as well. Therefore this lack of endemic infectious retroviruses in humans is inconsistent with evolution:

Other than the recent introductions of HIV and human T leukaemia virus (HTLV) into humans from other animals, humans seem to be devoid of species-wide endemic infectious retroviruses. By contrast, like most other mammals studied, other hominids and non-human primates (NHPs) do have such viruses. Indeed, given the remarkable corroboration between the phylogenetic trees of primates and their lineage-specific simian foamy viruses (SFVs) our common ancestors with other hominids almost certainly had SFVs. The same is probably true of the lineage-specific simian infectious retroviruses (SIVs) found in most NHPs. Assuming that the common ancestors of hominids carried multiple endemic infectious retroviruses, how did the human lineage eliminate them? Given that humans remain susceptible to re-infection with both SFVs and SIVs from other hominids, this seems unlikely to be explained solely on the basis of more efficient host restriction systems. Rather, there seems to have been an episode in which the ancestral human lineage was somehow 'purged' of these endemic viruses.

In other words, the endemic infectious retroviruses do not align with the expected evolutionary pattern. The human lineage must, somehow, have been purged of these endemic viruses. Perhaps such a purging occurred, and future research may be able to strengthen that hypothesis. But as it stands, this evidence is not consistent with evolution.
Chimp-Human Genome Beneficial Differences Are Few
As noted above, evolutionists were surprised by the high similarity between the chimp and human genomes. With so few differences, how could evolution construct such tremendous differences? But not only is evolution limited to a relatively few genetic modifications to create the human, but according to evolution the majority of even those modifications would likely have had little or no consequence or even would have been slightly harmful. Here is how a 2005 paper on the chimpanzee-human genome comparisons put it:

In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.

The paper is written from an evolutionary perspective, assuming that humans and chimpanzees share a common ancestor. Given that a priori assumption, they were forced to conclude that most of the mutations affecting protein-coding genes led to "neutral and slightly deleterious alleles." So not only are evolution's random mutation resources meager, in terms of both quality and quantity as explained above, but even worse, those mutations mostly led to "neutral and slightly deleterious alleles."
In fact the beneficial mutations in protein-coding genes, which presumably would be important in evolving the human from a small, primitive ape, literally number only in the hundreds. It would be astonishing if the human could be evolved from so few mutations.
Chimp-Human Genome Differences Have Discrepancies
Furthermore, the chimp-human genome differences show some strange patterns, with unexplainable variation towards the ends of most chromosomes, and with the chromosomal banding patterns.
A common response from evolutionists is that these discrepancies are small in magnitude. That is true, they are small in magnitude. But that is not what counts. Molecular spectra that make magnetic resonance imaging (MRI) possible are also small in magnitude. That doesn't mean they don't count. What is important is that the chimp-human genome differences show patterns that evolutionary theory struggles to account for. The evidence is not consistent with the theory, by a wide margin.
The chimp-human genome differences have also been described using sliding 1-Mb windows. Those results also showed nonrandom variations, but later research found that those variations correlate with the observed de novo human mutation rate patterns. The research paper concluded that the variation in chimp-human genome differences "is only partly explained" by the mutation rate patterns. But these results raise the specter that the variations in the chimp-human genome differences seen in 1-Mb windows may be explainable by a known phenomenon.
This suggests the possibility that future research may also explain the variation towards the ends of chromosomes, and with the chromosomal banding patterns. But that was not the claim. Evolutionists such as Venema claim that today's evidences "strongly support the hypothesis that our species arose through an evolutionary process."
Chimp-Human Alternate Splicing Differences
You may have learned in your high school biology class that genes are segments of DNA, but it is a bit more complicated than that. For starters, in the higher species a gene is often not a simple continuous segment of DNA but rather is interrupted several times by intervening segments. So there are the coding segments (called exons for expressed regions) and then there are the intervening segments (called introns for intervening regions).
When a gene is transcribed, the transcript contains both the exons and introns. It is then spliced by a complicated spliceosome machine that removes the introns from the gene copy and glues the exons together.
One of the features of the exon/intron genetic architecture is that it allows for alternative splicing schemes. In fact, incredibly, a given gene can have thousands of different forms depending on how the spliceosome machine edits the gene.
When it was discovered that the human genome contained about twenty five thousand genes it seemed too few. Are not more genes required for a human body? More recently it has been discovered that we make up for that small number of genes with alternative splicing schemes. Most of our genes may undergo such editing, and the result can be a completely different function for the resulting protein.
We have an enormous alternative splicing program in our cells, far more than chimps have. And this is another inconsistency with evolutionary theory.
Given the high similarity between the chimp and human genomes, and the relatively few beneficial mutations in protein-coding genes (discussed above), evolutionists have considered the possibility of evolution by splicing. In other words, our enormous alternative splicing program may have been an important factor in our evolving from a small, primitive ape.
But there are many thousands of these gene-splicing changes that would have to evolve. And unlike bacteria whose populations are large and generation times are short, our gene splicing changes would have to evolve in smaller populations with longer generation times.
It is difficult to see how evolution would have the resources to make this happen. The problem quickly becomes astronomically improbable if groups of genes would need to implement their new splicing logic together. And how could that not be the case?
In fact, even if only the order of implementing splicing for a small number of genes is important, the problem quickly becomes astronomically improbable. And again, how could that not be the case?
But this is only the beginning. In addition to the fact that the evolution of our enormous gene splicing changes is unlikely, it also represents an enormous serendipity problem. We would have to say that random mutations constructed complicated genes, with exons and introns and splicing codes, and the incredible splicing machinery, which, it would just so happen, would luckily be just what was needed to evolve humans.
It is even worse than this when one considers the exons themselves. Those random mutations would have divided the genetic instructions into so many exons, and it just so happened that they would be the right building blocks that, when rearranged, would lead to humans. The serendipity is astronomical here.
Imagine if you were building a tricycle and your friend modified each part you had crafted (not adding anything), and now the parts fit together to construct the space shuttle rocket motor.
The Kangaroo-Human Genomes
In my previous article I explained that, in addition to striking differences in otherwise allied species, striking similarities in otherwise distant species are also inconsistent with evolution. This problem arises also with the human genome. Consider the kangaroo genome, which turned out to be similar to the human genome. As one evolutionist explained:

There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order. Which really surprised us, we thought they'd be completely scrambled, but they're not, there's great chunks of the human genome which is sitting right there in the kangaroo genome.

It was a surprise because under evolution humans and kangaroos must be quite distant relatives. Evolutionists believe a small mouse-like species split into two lineages -- the marsupials and the placentals -- about 150 million years ago. And according to evolutionists that mouse-like species eventually evolved by random mutations into, among other things, a kangaroo in the one lineage and into a human in the other. With that much evolutionary distance the kangaroo and human genomes should have evolved substantial differences.
Conclusion
The genomes of primates do not support evolutionary theory. As we have discussed, there are always speculations for whatever evidence is discovered. Perhaps evolution did this, perhaps it did that. But that does not change the fact that the primate genomes do not "strongly support the hypothesis that our species arose through an evolutionary process," as Venema and fellow evolutionists claim. There are a wide variety of substantial contradictions and problems with this theory.