Genetically modified crops

As someone who has a high number of liberal friends on his social media outlets, I frequently see anti-Monsanto and anti-genetically modified food posts and pictures. Just this weekend there were all sorts of protests, including in my home state. Now here’s the thing: I don’t get it.

I’m not one to defend large corporations (which, incidentally, are not people but rather government-defined entities), but I’ve never considered myself part of the anti-Monsanto crusade that’s out there. I understand the desire to label food as a matter of general principle, but I’ve seen scant evidence that GM food holds any characteristics that should cause alarm. Indeed, I once saw a poll where one of the major reasons people were weary of such food was because it had DNA in it. Come on. That small family-owned farm with the kindly old couple that’s been growing organic potatoes for the community for decades is serving up a big healthy dose of DNA every season.

I also understand the misgivings people have about some of the lawsuits Monsanto has out there, but from what I’ve read, it’s all been greatly exaggerated. They certainly have a huge advantage in the market place by virtue of their size and wealth, but I’m not convinced they’ve been particularly unfair to other farmers. (Though I do worry about legislation for which they lobby. But that’s a feeling I have regarding every corporation.)

I’d be interested to learn what all this fuss is really about. I don’t think anyone has nothing but ulterior motives here, but I do wonder how much of the outrage is based upon legitimate concerns and how much is based upon the dissemination of false information.

Opening the St. Croix to alewives

The Maine legislature occasionally gets it right. This is one of those times:

The Legislature passed a bill Wednesday to end an 18-year blockade that has prevented alewives from running in most of the St. Croix River.

L.D. 72 passed the Senate by a vote of 33-0. The House voted 123-24 to enact the measure. The margins are sufficient to enact the emergency bill with Gov. Paul LePage’s signature.

If the governor does sign it, the bill will take effect immediately and allow spring runs of alewives through the fishway at the Grand Falls Dam near Princeton, in Washington County, and through much of the St. Croix watershed.

(The St. Croix is an important Maine river that serves as a border between the U.S. and Canada, winding through the edges of Downeast Maine, and emptying into the Atlantic.)

If you’ve wondered why the lobster industry in Maine (which, c’mon, is the only one that matters) has been reeling so much lately, one of the reasons has to do with alewives. This fish is a vital source of food for large predators, but it hasn’t been as easily available to them due to population declines and poor wildlife management decisions over the years. As a result, it is a strong possibility that there are fewer large predators in the Gulf of Maine, thus allowing a free-for-all explosion in the lobster population; the cockroaches of the sea aren’t being as vigorously hunted by non-humans as they once were. This ultimately drives prices down, hurting Maine fisherman. However, now that we can expect dramatic increases in alewife numbers, we should begin to see improvements in one of Maine’s key economic sectors.

Creationists should stay away from biology

I try to avoid the content Jack Hudson’s blog. He doesn’t write anything of value and he hasn’t any credentials in the areas that seem to be slightly interesting to him (namely biology), but I often poke over there to see if I can find any interesting bloggers in his comments. Unfortunately, this involves me skimming his posts. (After all, if he writes about a topic that doesn’t interest me, I may not be interested in whoever might comment on it.) And once in awhile, I fully read his shorter rants. Take a look at one his his recent examples:

Often when I argue that cells are infused with information driven molecular machinery and that this observation constitutes the basis for a readily falsifiable theory on why the cell is the product of the effort of a mind, opponents will accuse me of over-extending the use of the word ‘machine’. That is why I appreciate animations like the one below – it clearly depicts a molecular motor, that has been an integral part of cells since the beginning of life. It is clearly a mechanism composed of multiple integrated and highly interdependent parts that both convert energy into work, and provide the fuel on which the rest of the cell subsists.

The ATP synthase is definitely an information driven molecular machine, and the best explanation of its existence is that it was designed by a mind.

I can be brief here: biology is all about shape. Again and again, anyone who has studied the subject will quickly recognize that the only way anything gets done is through the interaction of molecules of the correct shape. The only exception is when we’re talking about ion gradients or something sufficiently similar where the cause of action is an electrochemical gradient (or, again, something sufficiently similar). And even then, shape is often still relevant in moving stuff from one place to another.

When it comes to ATP synthase, the basic idea is that a phosphate molecule binds to an ADP molecule and causes a conformational change. This isn’t information (which, incidentally, is a concept Jack has never been willing to define in scientifically coherent terms). It’s a change caused by certain molecules of a certain shape with certain properties, coming together to form a new shape with new properties. And if we back the train up a little bit, we’ll see that that is the case for the previous molecules, and the previous molecules to those, and the previous…and so on until we aren’t talking about much more than very basic chemical bonds.

How should we treat cloned Neanderthals?

Harvard geneticist George Church was recently interviewed by a German magazine where he said that we need to start talking about the ethical and other implications of cloning a Neanderthal. He said that, whereas the technological possibility is foreseeable in the relatively near future, we need to start the conversation today. Unfortunately, English-based media sensationalized his comments and falsely claimed that he was looking for a surrogate mother:

Harvard geneticist George M. Church was quoted in the Daily Mail as looking for an “adventurous woman” to serve as a surrogate for a “cloned cave baby.” The shocking headline spread quickly across the media with no small amount of help from major news aggregators like the Drudge Report…

“I’m certainly not advocating it,” Church told the Herald. “I’m saying, if it is technically possible someday, we need to start talking about it today.”…

Church added that he wasn’t even involved in the particular aspects of the Human Genome Project focused on Neanderthals. Nonetheless, he hopes to use the mistake made by the media for the greater good. “I want to use it as an educational moment to talk about journalism and technology,” he said.

To compound the mistake made by the media, people like Arthur Caplan, writing for CNN, continues to spread falsehoods even after the correction has been made:

Despite a lot of frenzied attention to the intentionally provocative suggestion by a renowned Harvard scientist that new genetic technology makes it possible to splice together a complete set of Neanderthal genes, find an adventurous surrogate mother and use cloning to gin up a Neanderthal baby — it ain’t gonna happen anytime soon.

My beef is with the baseless accusation that Church was being intentionally provocative. Here is what he actually said:

SPIEGEL: Mr. Church, you predict that it will soon be possible to clone Neanderthals. What do you mean by “soon”? Will you witness the birth of a Neanderthal baby in your lifetime?…

SPIEGEL: Would cloning a Neanderthal be a desirable thing to do?

Church: Well, that’s another thing. I tend to decide on what is desirable based on societal consensus. My role is to determine what’s technologically feasible. All I can do is reduce the risk and increase the benefits.

In other words, the magazine asked him all these things. He gave pretty uncontroversial answers, even choosing to take a rather neutral stance when asked if we should clone a Neanderthal. I think the evidence is clear that not only was Church not being intentionally provocative, he was actually attempting to give benign answers.

At any rate, this all does raise the interesting question of how we would treat Neanderthals if we did clone them. Would we give them the same rights and protections? Would we develop a new application for the old scourge of apartheid? I’m not sure the answers to these questions, but I do have some input on how we should go about considering them.

Humans are awfully fond of talking about our special status in the animal kingdom. Indeed, many of us refuse to even consider ourselves animals, disregarding the affront to biology such a stance is. Of course, we have some good reasons for separating ourselves, at least in the context of morality and ethics. Though such practices, common across many taxa, are little more than game theory working itself out amongst genes and individuals, humans take it to another level. So while, for example, our ape cousins will show rudimentary understandings of right and wrong, we have far more complex rules for our society, rules that we can reason out and justify by way of our higher level of intelligence. We are different and that’s important.

How different, though, are Neanderthals? We know a fair amount about them, but they haven’t been around for 20 or 30 thousand years. No one has interacted with them, so a cloned baby would be an experiment in every sense of its life. How different would it be? Would we have criteria established that said, ‘If the Neanderthal is different in these certain ways, it will not enjoy the same rights afforded everyone else under our laws’? I don’t know, but the concern is an interesting one because it raises the issue of why we think we’re so special.

Evolution is a continuous process. We are descended from species which were not human, but at no point did one species give birth to a brand new one. Every mother gives birth to offspring that are categorized in the same way she is. However, when enough time has passed, we’re given the luxury of defining different groups as species within this or that Genus under one or another Family. But look over the tape of evolution and everything eventually converges and lines blur. Just think about human evolutionary history: Back things up 100,000 years and we’re largely the same. How about 150,000? 300,000? 1,000,000? At some arbitrary point we pick, we’re going to start defining significant differences, but if we continually shrink the window of time, the differences start to disappear. (This is all a huge problem, in my view, for the Catholic or other theistic evolutionist who believes only humans have souls.) So from 500,000 years ago to 100,000 years ago, there will be notable change, but that change will be smaller between 400,000 and 200,000 years ago. And the differences become less when we look at our history from 300,000 to 200,000. Keep going and we may be talking about how different our ancestors from 272,000 years ago were from our ancestors living 271,000 years ago. Forget that our investigations into the history of life can’t get that specific. What’s important is that we have to realize there is no line in the sand that says “Species A ends there and Species B begins here”.

So if we do decide that Neanderthals are less deserving of the rights given to humans, we have to admit that humans, at some point in our lineage, were also not deserving. That is, our intelligence and consciousness become more and more comparable to our cousin apes (and now extinct man-like cousins) as we go back in time; we eventually arrive to a point where we would not give our ancestors the same rights that we enjoy. That means we are not inherently special, and I think that’s a major blow to a lot of our assumptions. The supposedly humble Neanderthal shines light on our human arrogance.

Leopards

I recently watched a Nature special about leopards that was absolutely fascinating. Of all the big cats, it seems that leopards may be the most intelligent, relying on cunning more than muscle. If you have an hour, here’s the video:

I’ve always thought of leopards and their non-immediate kin of pumas, cougars, and jaguars as little more than small, solitary lions: strong, fast hunters that rely on brute force. Not so. They lurk in the shadows, hiding from troops* of baboons and other potential enemies. When they make a kill and a clan** of hyenas wants a piece, leopards have little problem giving up their entire meal. They don’t go looking for a fight.

Unsurprisingly, leopards are doing spectacularly well. (This fact may vary for their taxonomic Family I’ve mentioned, but if so, only very slightly.) Whereas lions, cheetahs, and tigers face serious threats to their overall numbers, leopards enjoy a population of around a half million. Even the black panther (of the leopard variety) seems to do okay, despite its seemingly detrimental recessive gene.

I think a lot of people appreciate the awesomeness of big cats like lions and others when they seem them taking down a large animal, but leopards don’t seem to enjoy quite the same esteem. That has been true even of me (at least until now). I think part of the reason is simply how difficult it is to record these beasts. They’re quite wary of everything that isn’t food, and that includes humans. This would make particular sense if our ancestors treated them the way our ape cousins do. (Yet despite this wariness, they do often live very near humans, even invading villages with utter stealth on a frequent basis.) It really is a fascinating animal.

*A group of baboons is also known as a congress. They cooperate better than ours, though.
**Appropriately, a group of hyenas is also known as a cackle.

Convergent evolution

I was hunting around for some blogging ideas recently when I came across this post by Wintery Knight. It’s basically a copy and paste job because Mr. Knight is not qualified to speak of anything in biology (and he has amply demonstrated as much). However, the person he extensively quotes, Cornelius Hunter, is also 100% unqualified to analyze the world of biology. I’ve written about Hunter in the past.

As in his last post that just barely merited a response, Hunter makes a series of confused remarks about convergent evolution. (For those who don’t know – such as Hunter – convergent evolution is the process by which species of usually distant relatedness will acquire the same trait independent of their last common ancestor.) Let’s take a look at how Hunter mangles this:

The theory of evolution states that the species arose spontaneously, one from another via a pattern of common descent. This means the species should form an evolutionary tree, where species that share a recent common ancestor, such as two frog species, are highly similar, and species that share a distant common ancestor, such as humans and squids, are very different. But the species do not form such an evolutionary tree pattern. In fact this expectation has been violated so many times it is difficult to keep track. These violations are not rare or occasional anomalies, they are the rule.

Hunter is only leading into his mention of convergence here, but he’s already off to an embarrassing start. He’s attempting to claim that we don’t see an expected pattern of descent because that pattern is premised on the idea that similar traits must come from closely related organisms. He is factually incorrect. All he has described here is one method for determining relatedness between species: morphology. And even then, he has grossly over-simplified the process. For instance, take the skull of a dingo versus the skull of a Tasmanian tiger. They resemble each other quite closely, but they aren’t exactly the same. The latter has two holes in the roof of its mouth, a characteristic of marsupials. Go further and one will see that they also have different genetic codings.

Many examples are the repeated designs found in what, according to evolution, must be very distant species. Such evolutionary convergence is biology’s version of lightning striking twice. To explain this evolutionists must say that random mutations just happened to hit upon the same detailed, intricate design at different times, in different parts of the world, in different ecological niches, and so forth.

Were Hunter to take a peak at the genes in a Euphorbia, he might notice that they are markedly different from the genes in a cactus. That’s because, while both plants are prickly desert survivors, one is from the Malpighiales order whereas the other is from the Caryophyllales order. They have significantly different genotypes, but similar phenotypes. In other words, Hunter’s argument that random mutations are always hitting “upon the same detailed, intricate designs at different times, in different parts of the world, in different ecological niches” is not only verbose, but entirely wrong. It would be as though he said home builders have hit upon the same intricate design because some use cellulose insulation while others use spray foam. It’s the same result by a different means.

Everyone has heard of the kangaroo and its pouch. It is a marsupial—mammals that give birth at a relatively early stage in development, and then carry their young in a pouch. There are a great variety of marsupials that are curiously similar to a cousin placental species. The flying squirrel (a placental) and the flying phalanger (a marsupial) are one such example. Because of their reproductive differences evolutionists must say they are distantly related on the evolutionary tree. Yet they have strikingly similar designs which must have been created independently by random mutations. Every mutation leading to the two different species must, according to evolution, have been random (that is, independent of any need). No, natural selection doesn’t help.

First, his mutation argument is still wrong. Second, it isn’t merely reproductive differences that tell us the flying squirrels (which are two independent groups of rodents) are different from the flying phalanger. There is also evidence from their genetic relatedness, not to mention the obvious fact that one is placental and the other a marsupial. Third, of course natural selection is relevant here. That’s the whole reason two species are able to converge on the same solution to similar problems; natural selection has found an efficient solution to one problem faced by two species.

Though evolutionists sometimes deny biological convergence, it is a scientific fact.

I don’t know what Hunter is talking about, but that’s okay because I don’t think he does either.

He goes on to quote from a recent paper:

In mammals, hearing is dependent on three canonical processing stages: (i) an eardrum collecting sound, (ii) a middle ear impedance converter, and (iii) a cochlear frequency analyzer. Here, we show that some insects, such as rainforest katydids, possess equivalent biophysical mechanisms for auditory processing…

Thus, two phylogenetically remote organisms, katydids and mammals, have evolved a series of convergent solutions to common biophysical problems, despite their reliance on very different morphological substrates.

Now, remember the crux of Hunter’s opening: Similar morphology is the same thing as intricate design, thus Jesus. Yet here we see a “reliance on very different morphological substrates”. That is, natural selection in some insects has hit upon the same broad method for attaining hearing as it has in mammals, but it goes about the process in a largely different way, relying upon the insect phenotype it has already given itself. So not only is Hunter’s argument wrong from the get-go, but even if we’re generous and grant him his incorrect basis, he still gets blown out of the water. He has managed to somehow be wrong in his wrongness.

It’s one thing when someone branches into biology from time to time, relying upon the insight of others. We see that with Wintery Knight (the reason being that he hasn’t a clue about the field). We can’t expect everyone to be an expert, even if they should know better. However, Cornelius Hunter is another story. This is a guy who fancies himself qualified and reasoned, able to break down complex scientific ideas. Yet what we see is a man unable to even come remotely close to getting much of anything right about a relatively simple idea. And he keeps trying, getting things wrong every. single. time.

One way to help developing nations

The ways in which a person can make a difference in a developing nation are seemingly endless. Peace Corps, donating, fund-raising, awareness-raising, volunteering, and on and on it goes. But one of the best ideas I’ve heard has to do with cookware.

Quality nutrition is one of the biggest problems facing any developing nation. Every year people die from malnutrition, especially children. Others go blind from things such as vitamin A deficiency – something which can be remedied quickly and easily, if caught early enough, with a single shot that lasts years (because vitamin A is stable in the human body, and thus we are able to store it). And then others suffer from iron deficiency, something many of us avoid without even realizing it every time we eat our Wheaties in the morning. This last point is where the cookware enters the picture.

It was once common for pots and pans to be made of heavy iron, but soon after the industrial revolution took hold and steel and other metals became cheap, manufacturers began putting out lighter, and often more aesthetically pleasing, cookware. One effect of this was the need for greater iron in the diets of some people because the iron from their pots was no longer making its way into their spaghetti and potatoes and whatever else they were cooking. I think the next step here is obvious: Encourage greater use of iron cookware in developing nations. Of course, there is a cost associated with this, but the great thing is that this is a long-term solution for some people. Iron pots and pans tend to last a long time, after all.

Now, this is just one idea for one issue. There are plenty of more ways to address the poverty and problems of developing nations – for instance, more infrastructure – but a good place to start is by taking a look at the Millennium Development Goals set forth by the U.N. There really is so much to be done.

Fun fact of the day

The term “junk DNA” is a misnomer. It refers to DNA that does not code for proteins – only about 2% of genes do that – but it unfortunately implies a uselessness of certain DNA. That really isn’t what biologists mean when they use the phrase (or, rather, when others use the phrase; it has been out of vogue amongst professionals for some time now). All they mean is that we have DNA which appears to have no function. This makes sense in the light of evolution since natural selection wouldn’t necessarily be expected to select against useless DNA. After all, why not just leave it there? Unless it constitutes a substantial energy drain, it doesn’t matter. (Note: I am not referencing conserved DNA.)

However, new research is showing that much of our noncoding DNA does serve important functions. Namely, it regulates the genes that do produce proteins. There is still a substantial portion of the genome that appears to have no function, of course. Moreover, there is useless DNA out there that doesn’t code or regulate anything (microsatellites come to mind). However, we’ll all have to wait for further research before we really know the full nature of the human genome.

Chromosome 2

It has been proposed and well evidenced that human chromosome 2 is the result of a fusion event between two chromosomes in our evolutionary past. Briefly, here is the evidence:

All great apes except humans have 24 pairs of chromosomes. We only have 23. That means we need an explanation for such a difference that dates back only a relatively short period of time (5-7 million years). As it happens, human chromosome 2 shows strong evidence of being two fused chromosomes. The way we know this is that all chromosomes have telomeres and centromeres. Telomeres are repeating units of DNA that serve to protect the ends (and therefore middles) of chromosomes, sort of like a good pair of shoes and a strong helmet. Centromeres are DNA units located somewhere between the telomeres of chromosomes, generally relatively close to the center. Their function is to help assemble the two parts of a chromosome during cellular replication and reproduction. In human chromosome 2, we see that there are actually two telomeres fused together in the center. There are also telomeres on the end, but between each end and the center are centromeres. That means we have three telomeres (one of which is fused) and two centromeres.

I bring this up because I was recently reading yet another excellent post by The A-Unicornist and he was dealing with this stuff:

ID is really nothing but an argument from ignorance – it claims that certain things simply cannot be explained by science, so it must be ‘best explained’ by a designer instead. Take for example this post from The New Creationist. I often point creationists to the Ken Miller video where he explains the Chromosome-2 fusion in humans, because it’s a perfect example of the theory of evolution making a falsifiable prediction that ended up being powerful evidence that evolution is true – something that ID has never done and in principle cannot do, which is why it will never be a science. Now, this “new creationist”, who incidentally sounds just as credulous as the old ones, argues that such a fusion is impossible – that the chromosome should never have been able to fuse at all.

Being that I’m not a biologist, I have no idea how to directly refute what he’s arguing. But it’s conspicuously odd that rather than, I dunno, ask a biologist or two (like, golly I dunno, write a letter to Ken Miller?), he simply frames his argument as though the unanswered question itself creates a major problem for the theory of evolution.

Since I’ve used chromosome 2 as an argument for evolution, I am familiar with the creationist responses. As such, I want to address what the blogger known as The New Creationist is arguing:

If the fused chromosomes in an end-to-end fusion are ripped apart by the centromeres during cell division and cells must divide to produce an embryo then how does an embryo develop with two previously fused but now ripped apart chromosomes? We know that the loss of just one chromosome would be lethal and here we have the loss of both of the two
fused chromosomes. If fused chromosomes do not make it through cell division then how could a fused chromosomal configuration be a result of common descent since there would be no descendants by a biological pathway. Such would be miraculous. Indeed, I believe it is a miracle not only because it can not be explained by any natural pathway but also because it is contradicted by experimental data.

What he is trying to say (and what he later says a little more clearly) is that two centromeres would cause division and assembly to occur in two separate places. This would be an all around mess that would prevent not only mitosis, but meiosis as well. So what could the solution be? Well, he answers it himself:

Now, it has been proposed that the deactivation of one of the centromeres in the fused chromosome would prevent the rupture and subsequent loss of the newly formed fusion…

And that is the case. One of the centromeres has been deactivated. One possible reason for this could relate to the fact that the area near the deteriorated centromere (the pericentromeric sequences) has gone through a large number of duplication events, but this isn’t known and requires certain confirming evidence around other deactivated centromeres. I don’t know if any significant research has been done in this area since the 2006 paper about chromosome 2.

The New Creationist continues:

…but this poses another equally lethal problem during the pairing off of homologous chromosomes.

Let’s say that if C2A fused with C2B forming C2 (which has 2 centromeres) in the paternal germ line, the male’s sperm. Now, that sperm would have to fertilize an egg where both C2A and C2B not having been fused would have to pair off with the paternal C2 BUT if C2 has been prevented from being ripped apart because one of its centromeres has been deactivation then the corresponding maternal C2B (or C2A) will not combine with C2 in the mother’s egg because that centromere would have been deactivated.

In other words, he is saying that if two ancestral primates had offspring with the fused chromosome, then that offspring would have 23 chromosomes whereas the rest of the population still had 24. Mating between the two could not occur as a result, thus the fused chromosome could never make it beyond a single generation.

The most obvious solution to this problem is that several members of a population experienced a fusion event. It could have been a completely chance event, or it could have been due to a particular mutation that had spread down the line. That is, my money is on a mutation existing in a population that caused the fusion between two specific chromosomes. Perhaps all the pericentromeric duplications (which pre-date the fusion event, incidentally) gave rise to a gene that was free to mutate neutrally in the population. After some time, it managed to survive the generations, and made a marked difference. (That’s what has happened, minus the specific duplication events, with Richard Lenski’s E. coli.) Or maybe a mutation popped up just out of completely random chance, as opposed to being connected to any particular type of event. It’s hard to say just how any of this happened, but there are good hypotheses to be had on the question.

To conclude, the first argument presented here was defeated before it was even made. One of the two centromeres was deactivated long ago, as stated in the original paper. Indeed, that very paper even suggested a correlating factor in centromere deactivation that could be useful for future research. As for the second argument, I’m going to give Mike the last word:

[T]he fact that an explanation is either unknown or not immediately apparent would not refute the fact that the theory of evolution made this falsifiable prediction, nor would it suggest that there cannot be a rational explanation at all. Our new creationist seems to think that because he does not know how to explain it that a rational explanation is not merely unknown, but in principle impossible. Ergo, Goddidit. That ain’t how science works, kids.