An Exaptated Pseudogene

Appropriately, for this attempt to return to timely updates, the first new DpSU – Pseudogene Plays Important Role in Cell Cycle, by Jeffrey Tomkins – is again related to junk DNA, just as the last one I did was about ENCODE. This article, however, is of the old type – it’s about a genetic feature, once “dismissed as junk DNA,” that has now been shown to have a function. Or, to quote Tomkins:

Once again, DNA sequence that was once thought to be nothing but a genomic fossil has shown itself to be vital to human survival. In this case, if the so-called pseudogene is not functioning properly, cell cycle dysfunction and cancer is the almost certain outcome.

A pseudogene looks like a gene – often another gene in the same organism – but has lost its original protein-coding function. The pseudogene of interest here is called “ψPPM1K,” and is a processed pseudogene. To make such a gene a normal gene (here, PPM1K) is transcribed into mRNA and the introns are stripped out as normal in the process of protein synthesis. However, instead of progressing further the mRNA is transcribed back into DNA which is inserted back into the chromosome. The result is a partial clone of the original gene, generally lacking introns and possibly other parts. Continue reading

Ever More Complex

A new type of DNA sequencing technology has been developed and used to identify and characterize key regions of the genome called “enhancer” sequences. These are novel DNA features that were once thought to be a part of the so-called “junk DNA” regions of the genome. These key elements are now proven to be part of the indispensable and irreducibly complex design inherent to proper gene function for all types and categories of genes.

Jeff Tomkins’ New Technology Reveals More Genome Complexity is one of those articles that hits you with the nonsense almost from the beginning. Deconstructing that opening paragraph we find that the first sentence is perfectly accurate. There do exist in the genome regions, called enhancers, which promote the expression of the gene(s) they are associated with. Enhancers have been known for some time – they were even taught in my biology class last year, so they must be ancient – but a new paper in Science talks about a new method for identifying these regions. Continue reading

piRNA

Today’s DpSU, by Brian Thomas, is called Newly Found Biochemical Is Essential for Life. With a title like that you could be forgiven for concluding that the élan vital had been discovered. However, the implications of the headline seems to oversell the real discovery more than a little. The angle that Mr Thomas is actually going for is, oddly enough, a variation on the most typical anti-Junk DNA argument. Continue reading

ENCODE at Last

Yes, this lot. It was inevitable, trust me.It’s taken longer than I expected and isn’t up to the quality (accuracy-wise at least) that I had been hoping from the delay, but Jeffrey Tomkins has finally written ENCODE Reveals Incredible Genome Complexity and Function. He opens:

Both the evolutionist and creationist communities are abuzz with the latest results from 30 simultaneously published high-profile research papers, proclaiming that the human genome is irreducibly complex and intelligently designed.

Poor quality though it may be, this article doesn’t waste any time. The primary ENCODE paper, stupid and misleading things though it may well have said, did not say that. Continue reading

Disposable DNA

Skip ahead to the ENCODE stuff if you don’t care for the Tomkins posts.

For his blog post for this week (or last, depending on how you look at it) Jeffrey Tomkins wrote Deleting “Junk DNA” – Does it Matter? I’ll let him explain some of the background:

Does deleting “Junk DNA” in laboratory studies, such as in mice make a difference? Interestingly, a colleague of mine just recently pointed out a paper in which exactly this type of research was undertaken. In fact the study is a few years old, and was done in 2004. However, after a search of the literature, I have not been able to find anything similar.

Because this paper, however, shows up prominently on the web as some sort of proof for “Junk DNA”. I felt that a brief review of the facts that were actually discovered in the research are in order.

I don’t think I’d ever come across the paper – Megabase deletions of gene deserts result in viable mice (pdf) – before, actually. But it does look like it could be useful in future. Let’s see if Tomkins can persuade me against it, shall we? Continue reading

Ultraconserved Elements

Another Jeffrey Tomkins post on Designed DNA? Oh, why not.

This one is called Ultraconserved DNA Elements – An Evolutionary Enigma. What are they?

Ultraconserved DNA elements are short chunks of genomic sequence 200 bases or more that are highly similar (conserved) among different types of animals and are generally noncoding (1,2). Hence, they should have very little evolutionary selective pressure acting upon them and evolve rapidly (3).

The first sentence there is correct, or as near to as needs to be,* while the second is not – and with that this post falls immediately. Continue reading

Evilution

The other day I wrote a post called Watch Who You’re Calling “Anti-Science”, in response to an ICR article that accused a chronicle of the evolution “controversy” exactly that. Today’s Daily (pseudo)Science Update declares to the world: Evolution Delays Discovery of Dolphin Sensory Ability. The irony is strong in this one…

Random dolphin pic from wikimedia Continue reading

Genetic Stop Sign Halts Evolutionary Explanations (DpSU)

Soo… If you genetically modify the good ol’ fruit fly, Drosophila melanogaster, to remove a presumed-redundant genetic ‘stop signal’ at one of the many places in the fly’s genome where there are double ups, you don’t get a very happy fly. Also, this disproves evolution. hmm…

You may have noticed that Mr Thomas has two default templates for his news articles. In the first – such as the baby tyrannosaur news item I covered at the end of this post, or the Io post – he takes a legitimate news piece and/or scientific study, and uses that as a launch pad to talk about something only vaguely related, usually something he claims ‘evolutionists’ cannot yet explain. Alternatively, in a post like this, he takes the study and reinterprets it to back up creationist ideas.

In this article, Thomas also talks about “a study published in 1980, [where] core fruit fly genes were altered, one by one, and the resulting plethora of dead flies proved that there was no “wiggle room” to add the mutations that evolution would require.” The 1980 study can be freely downloaded here, while the new one will require a subscription to Nature (which I don’t have, btw). When referring to the study Thomas links to an article here on the subject, if you want to read along.

The 1980 study deals specifically with mutations that affect “segment number and polarity in Drosophilia“. I would contend that tinkering with such genes is like randomly playing with the foundations of a house that’s already been built. Especially since all the mutations involve the removing of segments. As a general rule, major changes in the body plan of animals are rare, for the reason that other things have been built on top of this and rely on it to work, otherwise they become harmful. You can’t give a cat six legs – at the very least you’ll stuff up it’s finely evolved balance. It shouldn’t be unexpected that such mutations would be largely detrimental – evolution doesn’t progress in such large stages all at once.

As for the new study, this doesn’t really support Mr Thomas’ conclusions either. As I mentioned (to quote from the article on the study) “the majority of genes have more than one stop-signal” which looks at first to be redundant and useless. That we can show that there is a strong reason for this doesn’t mean that the organism cannot evolve. Basically, Thomas does not succeed in backing up his conclusions:

First, in addition to the raw code for proteins carried in the gene, this particular stop sequence is also required for any fruit fly to survive. In other words, the genes plus the regulatory DNA comprise an all-or-nothing system that defies evolutionary ideas of the fruit fly being the product of a gradual accretion of its parts.

Moreira said that both full stop signs are required for “effective regulation of the levels of the resulting proteins.”2 The correct numbers of proteins must be expressed during embryonic development.

Second, this result adds to an ever-growing list of regulatory DNA sequences that do not code for proteins but are nevertheless vital. It appears that a vast majority of any organism’s genome is highly regulated, tightly packed with information (often double-layered), and therefore unable to tolerate many mutations without breaking down.3

Citation 2 is from the alphagalileo.org article I linked to above, while 3 is from one of Thomas’ own articles, which is surprising as it seems to be related to Junk DNA, a common subject in the ID community at the moment, for some reason. There are therefore plenty of better places to cite for this important statement.

In summary, what Thomas is saying is that Fruit Fly genome is such that further modifications cannot be made by evolution as all mutations are detrimental. He is also extending this into the past, effectively claiming that the D. melanogaster genome is Irreducibly Complex. This is again a dangerously large example if IC – there could easily be a simpler form, considering what we know from the two studies. A lot of research has been done on D. melanogaster, and I don’t know if there has been other studies showing places where you can mutate the fly to get surviving offspring. I have a hunch though, that there have been documented cases of this.

So, Thomas is trying to show that “the removal of this one fly “stop sign” demonstrates that the whole fly must also have been purposefully engineered.” He doesn’t manage it. All we have is a study that shows it’s not possible to remove segments from the fly willy-nilly, while the other shows that a common feature of genes is infact useful, as you would expect. More evidence is needed to “prove that there [is] no “wiggle room” to add the mutations that evolution would require”. Until then…

Quick DpSU’s #1

Here’re some quickies:

Self-Cloning Lizards Fit for Survival

So, some lizards can reproduce by a system akin to cloning – parthenogenesis – and this can be created in the lab. Also, “evolution has no useful explanation for the origin of sexual reproduction, let alone unisexual.”

This isn’t useful in itself. Sure, the field is not settled, but what is? Ironically, the article itself gives us an idea for an explanation for why a species could reproduce both sexually and asexually:

It would make sense that a Creator would have endowed these egg-laying vertebrates with the potential to perpetuate themselves even in the event that a male was unavailable.

It would also make sense that a species could have both abilities due to natural selection. And anyway, the actions of a ‘Creator’ can always be made to ‘make sense’ in the light of new evidence. How is this a ‘useful explanation’?

Sounds like another “you can’t explain therefore God” article.

‘Old’ Galaxy Found in ‘Young’ Part of the Universe

According to Mr Brian Thomas, M.S., the author of most of the science related DpSU’s, a distant galaxy imaged via gravitational lensing as it was 800 million years after the Big bang is too modern in appearance to be from that time period, calling the whole Big Bang theory into question, claiming that “In the common conception of stellar evolution, 200 million years is not enough time for the Big Bang’s randomly distributed gases to have coalesced into well-formed stars and galaxies.” That the reference for this is, interestingly enough, from one or Mr Thomas’ own articles from about a year ago, which doesn’t provide any references of its own that would back up Thomas’ present claim. Even more interestingly, the citation has the following statement beside it:

Actually, the addition of time does not make star formation any more feasible. Since a nearby exploding star would be necessary to form a new star naturally, it stands to reason that the first stars—and therefore the galaxies that they inhabit—must have been intentionally created.

I was under the impression that the very earliest stars did not need any stellar shock waves to start off – they coalesced out of the abundant hydrogen and were very large, lasted for only a short while and blew up in a spectacular fashion, providing plenty of energy to get any nearby stars that did need a good jolt moving. It would also make sense if the reason why modern stars need such a shock is that, if they didn’t, the would’ve already have formed. I could be wrong, mind.

Original Study: (pdf)

Thomas’ source articles: here and here

He also seems worried (if that is the right word) about this new galaxy having “well-defined edges”. I’m not sure how he can tell (a more zoomed in picture doesn’t help), and I can’t find his source for that.

Evolutionary Leftovers in DNA? Not So, Says New Study

This is basically about Junk DNA (the titular Evolutionary Leftovers) which other people are covering in far more detalil than I am at the moment, so I’ll defer you to one of them

And finally, T. Rex Toddler Answers Noah’s Ark Questions

What? The whole the-whole-thing-couldn’t-actually-float-if-made-from-contemporary-materials thing? Or what they fed the animals on? How a colony of bees is supposed to recover from a population of a single queen and a useless drone? How small flightless birds such as the kiwi are supposed to have gotten from the far corners of the earth to Mesopotamia in time to catch a boat, and then back again? What all the trees were doing at the time? What the salinity of the water during the flood was, and what all the fish that didn’t like that amount did during that time? How the flood managed to carve out the grand canyon in one go without stripping the topsoil off the entire world at the same time? Where all that water came from, and where it went (without invoking divine intervention)? And for that matter, where did they put all the feces?

Apparently not. The article is trying to counter the old claim that there wouldn’t be enough room for all the animals on the ark, and does so in two ways.

  1. There could have been juveniles on the ark, rather than adults (hence the tying in with a new discovery of a “T. Rex Toddler”), cutting down on the space per animal (never mind infant mortality)
  2. There was only one pair of every kind on board, and so cutting down on the number of animals needed to be taken.

I haven’t done that math, but I doubt number one does anything to help the situation. On a related note, are Dinosaurs ‘clean’, and do they count as birds? (I know bats do). If so, then Noah needed not one but seven pairs of each.

As for number two, this is shaky ground. If only one pair of each kind was on board, then in the intervening period between then and now millions of species would have had to evolve, at a much faster rate than any ‘Evilutionist’ has suggested actually happens. And this from people who reject evolution utterly as having never been observed…