PaV

A new study has come out that tracks ‘tracks’; i.e., reptile ‘tracks’. It seems that the transition from a straddled to an upright position of reptilian limbs took place almost immediately. So scientists say that have studied fossilized tracks prior to, and immediately after, the end-of-the Permian mass extinction. [BTW, let’s remember that the Darwinian objection to an absence of intermediate forms is the imperfection of the fossil record, with the difficulty of ‘soft-tissue’ fossilizing as a partial reason. But here we’re talking fossil footracks, which would seem even harder to form, and yet they’re found!] Professor Mike Benton offers this: “As it is, the new footprint evidence suggests a more dramatic pattern of replacement, where the sprawling animals that Read More ›

In a just published article in Plos Genetics, Merdith, et. al., study the enamilin gene (ENAM) in four different orders of placental mammals having both toothless and/or enamelless taxa. Their results show that, indeed, the enamelin gene is basically in place in the toothless taxa, but that either “frameshift mutations and/or stop codons” are found in the toothless and enamelless taxa. They then use a “novel method based on selection intensity estimates” to determine whether molecular evolutionary history of ENAM would ‘predict’ the occurence of enamel in “basal representative of Xenartha (sloths, anteaters, armadillos)”, which contains many frameshift mutations. Their conclusion? Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide Read More ›

I just picked up this article at PhysOrg.com. The kinds of things that scientists are up to these days are quite interesting. Here’s a sample: Researchers design and build networks of genes, splicing them into bacterial genomes to run specific tasks or manufacture desired molecules – a process akin to installing biological computer software. Though the field is rapidly advancing, the gene-based tools available to synthetic biologists remain limited. I found the allusion to “installing computer software” quite compelling. Will these ‘synthetic biologists’ be the ones to settle for us the question of whether intelligence is present in the genome? This work is in the May 29th issue of Science, for those who have online access.

I’m just posting this to give people an update on what researchers are finding. More and more, so-called “junk DNA” is proving to be essential for life. Here, transposons, considered, generally, to be the “junkiest” of the “junk”, is found to have a rather central role in the development of a pond critter. Here is the write-up on PhysOrg. com.
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Here at UD we’ve heard over and over again that unless we “know” who the Designer is, then we can’t infer design. For example, if we were to argue that we’ve never seen the ancient Native Americans who fashioned arrowheads from stone, yet we are able to infer design in arrowheads nonetheless, the Darwinian side would respond saying, “Yes, but that’s because the Native Americans are humans like ourselves.” PhysOrg.com has an article about the microRNA, miR-7, which has been found to regulate a network which brings about uniformity among humans. The article is interesting in itself, but most interesting is this comment by one of the lead authors, Richard W. Carthew: When something is changed, say the genetic sequence Read More ›

PLoS Biology has an article out today entitled: “Hotspots of Biased Nucleotide Substitutions in Human Genes”. I’ve mentioned this ‘biased’ substitution pattern before. What the authors see, they tell us, is a definite W->S substitution pattern in human genes (Weak to Strong = A:T->C:G) against an overall pattern of S->W; for the entire human genome. This is part of their summary: Our findings are consistent with a model of recombination-driven biased gene conversion. This leads to the provocative hypothesis that many of the genetic changes leading to human-specific characters may have been prompted by fixation of deleterious mutations. What the authors report is a non-random shifting within genes, and the introduction of “deleterious” mutations. Neither of these is consistent with Read More ›

I’ve been reading Paul Davies’ book, The Goldilocks Enigma (published in the U.S. as “Cosmic Jackpot”) over the last week or so. I would recommend it to anyone who wants a full appreciation of scientist’s thinking about the world we live in. Davies is, IMO, the best expositor of the ‘popular science’ book. He blends, better than anyone else I’ve read, the more technical aspects of physics and real-world analogies that help one to grasp the technical depth he presents.

The Goldilocks Enigma is about what we would call the “anthropic principle”. But Davies, if you will, ups the ante with the inclusion of the implications he says derive from treating ‘dark energy’ in a quantum mechanical way (that is, including so-called ‘quantum fluctuations’). While all of life seems, from the free parameters that we measure, ‘fine-tuned’, the greatest ‘fine-tuning’ comes from the calculation that one does to determine the density of dark matter assuming quantum fluctuations all across the electro-magnetic spectrum up to, and including, EM waves having Planck length (about 10^-33 cm). This calculation results in a density figure of 10^93 grams/cubic centimeter. What is the actual density of dark energy as actually measured? 10^-28 gram/c.c. Thus, the calculation is off by a factor of 10^120. Davies also tells us that calculations have been made indicating that if the dark energy density was off by a factor of 10—that is, if it was 10^-27 instead of 10^-28, then galaxy formation would not be possible; and, hence, no life. This means that dark energy density is ‘fine-tuned’ to one in 10^120.

This last number gets Davies’ attention. Here is what he writes:

“Logically, it is possible that the laws of physics conspire to create an almost but not quite perfect cancellation [of the energy involved in the quantum fluctuations]. But then it would be an extraordinary coincidence that that level of cancellation—119 powers of ten, after all—just happened by chance to be what is needed to bring about a universe fit for life. How much chance can we buy in scientific explanation? One measure of what is involved can be given in terms of coin flipping: odds of 10^120 to one is like getting heads no fewer than four hundred times in a row. if the existence of life in the universe is completely independent of the big fix mechanism—if it’s just a coincidence—then those are the odds against our being here. That level of flukiness seems too much to swallow.” (italics in the original)

Well, anytime someone starts talking about science and coin flips, IDists are interested.
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In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.” Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of Read More ›

Over at Panda’s Thumb, they are taking issue with the values for selection probabilities of neutral and advantageous mutations that Sal has taken from Kimura and Ohta’s “Theoretical Aspects of Population Genetics”. Since there was a link that provided a ‘look-see’ inside the book, I did so. Well, what I found was very fascinating.

Kimura and Ohta give a very brief overview of the entire field of population genetics up to the time of their writing (1971), distinctly admiring the pioneering work of R.A. Fisher, but not following it because it uses a more sohpisticated “branching process”, and because his model assumes an “infinite” population size. So they write the following:
“. . . [Haldane’s] results allow us to make statements as ‘it takes about 1,000 generations until the gene frequency changes from 0.7% to 99.3% with selective advantage s= 0.01’. . . .

“More than 30 years after publication of Haldane’s paper (1927b), we have finally begun to understand more about the fate of individual mutant genes in terms of the powerful diffusion methiods based on the Kolmogorov forward and backward equation (cf. Kimura 1964). In particular, the average number of generations until extinction, and also the time until fixation of an individiual muatant gen in a finite population have been workd out (Kimura and Ohta 1969a,b).” Read More ›

It a newly issued study in the PNAS, a species of lizard was transplanted 36 years ago from one island in the Adriatic to another. Tremendous phenotypic changes have occurred, the most dramatic, in my estimation, being the development of ‘cecal valves’ in the digestive tract to be able to digest the plant food that the transplanted species of lizards has taken to eating. Cecal valves occur in only 1% of all lizard populations, yet it developed in only 36 years—along with changes in head size, jaw size, and bite strength (needed to chew the cellulose found in plants)!

There seems to be two ways of looking at this: (1) that NS has brought all of these changes about; or (2) the environment, specifically the proteins/enzymes/chemicals of the plant life on the new Adriatic island has interacted with the genome to quickly bring about these changes. Considering Haldane’s Dilemna–much discussed here at UD–there have been simply too many changes that have occurred to the physiology of these lizards for NS to be invoked as the cause. Additionally, if NS “can” work this fast, then why aren’t we seeing the development of higher taxa of animals and plants right now? The old argument is that NS works too slowly to be seen, and that’s why we don’t see these higher taxa—nor the intermediate forms which would be required—in present day flora and fauna.

What we seem to be seeing isn’t exactly Lamarckism, but a kind of form of it: i.e., the environment produces changes in the phenotype of the lizards which is inheritable, but is doing so via genetic regulatory mechanisms; IOW, epigenetics.

The more we learn, the harder it is for RM+NS to keep up.

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Here’s an article from PhysOrg saying something that has been said on this blog for years. The experimenters were working with gold crystals, trying to build different structures. Here’s some of what they write in this summary article: “He likens the process to building a house. Starting with basic materials such as bricks, wood, siding, stone and shingles, a construction team can build many different types of houses out of the same building blocks. In the Northwestern work, the DNA controls where the building blocks (the gold nanoparticles) are positioned in the final crystal structure, arranging the particles in a functional way. The DNA does all the heavy lifting so the researchers don’t have to.”

Experimenters have recently found that genes–whereby they mean particular sequences of DNA–can “find” one another without the intervention of proteins or other factors. It appears to be strictly an effect caused by electrical charges along the DNA strand; the longer the ‘gene’ (that is, sequence length), the greater theapparent ease in ‘finding’ one another. The experimenters feel that this finding is a help for figuring out what happens during homologous recombination.

Here’s part of what they say: The researchers observed the behaviour of fluorescently tagged DNA molecules in a pure solution. They found that DNA molecules with identical patterns of chemical bases were approximately twice as likely to gather together than DNA molecules with different sequences.

Professor Alexei Kornyshev from Imperial College London, one of the study’s authors, explains the significance of the team’s results: ‘Seeing these identical DNA molecules seeking each other out in a crowd, without any external help, is very exciting indeed. This could provide a driving force for similar genes to begin the complex process of recombination without the help of proteins or other biological factors. . . .’

The article from ScienceDaily is here.

I have an OOL question: This study strongly suggests that similar DNA sequences have a preferential attraction for one another. And the longer the similar sequence, the greater the attraction. If that is the case, then, if a particular ‘gene’ began to ‘replicate’, wouldn’t the replicated ‘genes’ congeal together?

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Because of a prediction, a very strong prediction, I made on another thread, I’ve had reason to look into just what has been happening to Darwin’s finches way off on the Galapagos Islands.

Here is a paper published last year in Science Magazine by the Grants, experts in Darwin’s finches. I looked at their paper, looked at their data, and have come to the conclusion that what I predicted as the ultimate explanation to changed beak sizes is the more reasonable interpretation of the data they present.

But before we even get to the data, here’s a remark from a National Geographic website review of the article that supports my basic position:

“ Researchers from New Jersey’s Princeton University have observed a species of finch in Ecuador’s Galápagos Islands that evolved to have a smaller beak within a mere two decades.
Surprisingly, most of the shift happened within just one generation, the scientists say.”

The shift happened in ONE year? What kind of population genetics are at play here?

Well, to the data:
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Here’s a link to a PhysOrg.com article talking about ERV’s (“jumping genes” per Barbara McClintock) and the newly discoverd role they seem to have played in primate evolution. Here’s a quote from the link: “Now it appears that another level of evolution occurs that is not driven by point mutations. Instead, retroviruses insert DNA sequences and rearrange the genome, which leads to changes in gene regulation and expression.” Excuse me if I’m wrong, but this, it seems to me, is the kind of thing that would be helpful to discuss here at UD.

In this week’s Nature, an analysis of the human genome has shown tracing 4,692 homologous recombinations backwards in time leads to “24 distinct groups”. They say their work supports a “‘punctuated’ model of evolution.” I don’t have access to the entire article (maybe somebody does), but the language contained in the abstract is the kind that we might associate with “front-loading”; viz., “Our analysis reveals that human segmental duplications are frequently organized around ‘core’ duplicons, which are enriched for transcripts and, in some cases, encode primate-specific genes undergoing positive selection.”

I did a Wikipedia search for “duplicon” and found nothing; but a Google search gives the following article: Abstract Only. Duplicons appear to be something that is seen at the chromosomal level, and involves low-level repeats of the chromosome. The description this week’s Nature authors give of a duplicon “enriched for transcripts” seems to strongly suggest that the rearrangements that have taken place in the “duplicon” have resulted in more of the genome being expressed. The image I have of what might be taking place comes from my very ancient familiarity with computer programming, and, assuming programming essentials haven’t changed much, it is this: in a computer program there are decision nodes and “go to” nodes that redirect the program to various subroutines, these subroutines being present at some numbered location along the length of the program. If for some reason one subroutine in the program were substituted for another, the program would probably still run, but the output would certainly be different. And, if additional “go to” nodes were “copied”, more subroutines would be expressed. Likewise, if you have genetic instructions along the string of nucleotides that redirects the genetic program to some other downstream part of the genome that allows some particular protein/regulatory function to take place, then, through recombination, different “subroutines” might be inserted, or more signals for transcription might be included.

Maybe this is straining the programming analogy, I don’t know. But in any event, what the authors are reporting doesn’t sound to me like information is being generated (gradualism), but that already present information is being more robustly used (punctuated model of evolution).

Any thoughts?

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